These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Ho Yay: Tokai. For example, when Kyoko's Dragon Ozaki needles him about "taking it up the ass" from his one-time protege Hojo:
Tokai: (smirking) "You should let him do you, too! It's not just your ass! It rattles your whole insides! Wham! Wham!" (to Kyoko) "You want Hojo to give it to you so bad you can't stand it, can you!"
And he has many, many other lines like this throughout the series.
All of the female characters are portrayed either as prostitutes, or a sexy lady one of the main characters have picked up, or models the politicians are having sex with, or ladies the yakuza are raping. Though there are two prominent female characters (Kyoko and an American politician, who demands Japan to drop their high import tax on American cars), their roles were later reduced where Kyoko ends up falling in love with Hojo and forgetting her mission to arrest him while the politician ends up sleeping with Asami which prompted her to drop her demands and leave the country.
Fan-Preferred Couple: While Helen/Druitt is canon Helen/Tesla is more favored both in and out of universe, especially by Tesla. Ascended to Official Couple in the last episode.
Fridge Brilliance: Ever thought that, for someone who tried to artificially extend his life so long in the first place, Watson was strangely accepting of his death in Revelations, what with him not even trying to fix his anti-aging suit when he knew it was failing? Well, thanks to Helen's time traveling back to the Victorian era in Tempus, Watson knew that he would be dead by the time period she came from, which he knows to be between 2010 and 2015 (from her driver's licence). So he always knew that he could extend his life only until then, no matter if he could technically make it last longer or not. Revelations aired in 2009.
Ho Yay: Druitt and Watson. Also qualifies as Foe Yay. Watson also seemed to have quite a bit of affection for Will, and vice versa. (Then again, Watson is played by PeterWingfield.)
Narm: Will's dance for Kali. It was a pretty cool dance though.
Most of what Will does after getting linked to Kali/Big Bertha. The torture scene was, in fact, downright hilarious, among other things; at least some of it had to have been deliberate.
In the Musical Episode, Abby's Villain Song is interlaced with Will dispassionately mumble-singing. Abby's near-death experience was similarly ruined by Will's solo. One thinks that this also must have been deliberate.
Narm Charm: As above, Will's dance for Kali. The fact that said dance is a full on show stopping Bolly Wood dance number has to mean they did it on purpose. It's just too damn ridiculous to be an accident.
In-universe as well. Look at the crowd, none of them can see Will's imaginary dancers, yet none of them are in any hurry to stop watching him.
Special Effects Failure: Not the low-budget CGI (which is surprisingly decent) but the goofy-looking muscle suit that the lead actor wears when he's turned into a hulking freak in one episode.
They Just Didn't Care: One is tempted to think they didn't do research with their original claim about the Arthur mythos that makes the Morrigan a creation of Morgan Le Fay but actually they had to do some research to get that far, so one shall guess they just did not care.