Yuuko's wish being revealed to be Watanuki to continue existing after her vanishment, considering how biasé and occasionally fatalist she is about deaths, opens an interesting debate. While it's clear that the witch came to appreciate and love his worker despite all their quirks, the nature of her feelings is less clear about whether they were mentorly/platonic or more romantic in kind as Yuuko/Watanuki shippers defend.
Similarly, Watanuki's decision to wait for her during all the eternity seem to be quite significant on how important she was for him, considering he chose to devote his life to it despite the presence of more conventional love interests like Himawari and Doumeki.
The time Watanuki defends the spirit of an unborn girl who had been recently aborted. With the bad guys of the day being unrelated supernatural forces who want to steal her soul, the decision of abortion itself is treated as a sad but otherwise acceptable event, stating that every time a unborn child is aborted, their soul will be born another day.
Ass Pull: Himawari being Put on a Bus. The reason why she no longer shows up in the sequel comes out of nowhere and it's not even fully explained. It was never implied before that the shop was harmful for her and it's made perfectly clear that not a single person except for Doumeki can remain by her side without eventually suffering a terrible fate. In spite of this, she's happily married to what's implied to be a normal businessman and the shop she visited in the past suddenly hurts her whenever she enters. It's very hard not to conclude that CLAMP simply wanted to erase her from the series, likely because her role had been fulfilled.
There are those who solely enjoy the manga but dislike how Tsubasa -RESERVoir CHRoNiCLE- is intertwined with the plot, particularly with Yuuko's and (especially) Watanuki's pasts. The problem gets worse as in order to understand it, they have read the other manga, which is problematically confusing of its own. Others find it okay because it expands the world-building of both series and for them, it's easy to follow and understand if you read both series.
The manga's ending divided people. Some people believe that the series should have ended with Volume 16 as the last chapters did not build up anything to the story. CLAMP themselves acknowledged people's reaction to the ending and were happy since some wondered about Watanuki's fate.
×××HOLiC: Rei also divided the base. Despite that Yuuko is back, some people still find it more of a rehash of the earlier volumes without any new input on the story at least until the nature of the setting was revealed. Then, it went into a hiatus just to make room for Tsubasa World Chronicle, which anger several readers. And despite that the two mangas are still connected, some readers felt that Watanuki and rest would only get some cameo appearances. In April 2015, the manga went back to publication, though its schedule is somewhat sporadic and it still continues to leave many readers with mixed feelings. Meanwhile, others were glad that the series continued since several readers were disappointed with the ending of the original manga.
Shamisen/Plectrum. Which technically isn't a cargo ship since it's actually cat/butterfly. Maybe. It gets confusing when their human forms look like their owners. And it only gets more confusing when you realize that the bit of the plectrum's form we get to see looks very much like a certain deadexorcist.
The only universally accepted pairing within the CLAMP fandom is apparently Larg/sake.
Hollywood Homely: Watanuki, considering he's not particularly popular with human girls, but certainly isn't ugly to say the least. To be fair, the reason he isn't popular with girls probably has more to do with his flailing and screaming at things no one else can see than his looks.
Ho Yay: Once again, it's CLAMP. There's subtext not only between Doumeki and Watanuki, but also between Watanuki and Haruka, who he is much more willing to admit fondness for. In the first's case, CLAMP is certainly pushing "subtext" to its limit - hell, recent chapters have Doumeki and Watanuki alone in a bedroom, with Watanuki wearing a loose kimono, discussing about the mating habits of cats, and what it needs for the ideal mate and love; not to mention the above statement on how much Watanuki resembles a cat.
Judging by the hints given in Routen years or so have gone by, Himawari is married and only visits the store once a year, while Doumeki and Watanuki spend almost every afternoon together. Doumeki goes out to work, brings the groceries, Watanuki cooks and serves the food, then they talk about anything while Watanuki bends around the floor with his clothes almost falling off. Their relationship seems to have almost completely become that of a married couple if it weren't for Watanuki somehow managing to remain rather ambivalent.
The latest chapters have become increasingly homoerotic, such as when after granting a ghost woman the wish of being reunited with her long lost lover, Watanuki recieved an umbrella as payement and; while explaining to Doumeki that finding a beautiful woman under an umbrella is an amazing discovery for any man, he walks femininely under said object and winks at his friend. Whether this is CLAMP's subtle way of messing with our minds or something more remains to be seen, and most probably never will.
On the opposite end, Yuuko is a wee bit touchy-feely with one of the early clients, as well as the twins in one of the earliest chapters (even kissing one of them.)
Moral Event Horizon: If hurling a cup of boiling hot water at Watanuki for daring to befriend Kohane doesn't turn her mother into an irredeemable bitch in the eyes of the reader, then hitting Kohane on national TV should do the trick.
One True Threesome: A small minority of the fandom is quite dedicated to the Doumeki/Watanuki/Himawari threesome, due to the ways the three of them have been built to compliment each other and interact throughout the series. A decent amount of the fandom at least holds some fondness towards the trio and the Live Action Drama based on the series also decided to give their relationships the strongest focus.
Paranoia Fuel: The new series ×××HOLiC: Rei is responsible for this. The choice of setting including Yuko alive and Watanuki as her assistant even though the original the series ended with Yuko dead and Watanuki as the shop's owner is leading many people believe that the entire series is about Watanuki escaping from reality. Latest chapters appear to hint this as Yuko and Domeki, and later even Himawari are shown to be aware of Watanuki having to make an important decision while in chapter 23 Watanuki even talked like his ×××HOLiC: Rou persona much to his and the readers' confusion.
As of the latest chapters it's been revealed that Watanuki's subconscious, in the process of gathering some things for Syaoran from another dimension, had accidentally created the setting to emulate the time in his life when he was happiest, and that out of concern for his wellbeing, Himawari and Doumeki decided to follow and watch over him. Yuko on the other hand is heavily suggested to be a projection created by him, although it also seems that she in of herself developed a will identical to the "true" Yuko, enough so that one cannot be truly certain who or what she really was.
Ship Mates: Watanuki/Yuuko shippers often support as well the implied-canon-but-not-quite Clow Reed/Yuuko, citing Watanuki's resemblance to Clow due to being his descendendant as the reason of why she would see him through romance eyes.
Uncanny Valley: Occasionally the TV animation (and especially the movie) slips into this. One reader of Anime Insider wrote in after they featured Yuuko on the cover and asked, "Why did you put a sexy zombie on the cover?" and managed to just about sum up most people's grievances with the art in one sentence, while simultaneously spoiling a major plot point unintentionally.
Whole Plot Reference: A manga about a nervous, irritable guy with a mysterious background and the ability to see supernatural things, who works obligedly in a quirky shop for a sexy, worldy boss fulfilling weird jobs and missions related to the spirit world, often aided by an imperturbable guy with supernatural powers and a lot of subtext? It seems that CLAMP recycled the script of Drug & Drop.
The Woobie: Nearly every major character is a woobie in some form or another, Watanuki, Kohane and Himawari being the most prominent examples.