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.
The moment where Bernard and Fran duck under their restaurant table to find a miniature bar, complete with bartender, quite literally under everyone's feet is surreal even by this show's standards. They barely even acknowledge it, preferring to have an argument about how boring their dinner conversation with Manny's parents is.
The fly in Manny's First Day. It comes in, interrupting their conversation, lands on Bernard's desk for two seconds, then gets up and flies away, shutting the door behind itself....somehow. Then Bernard and Manny immediately resume their conversation.
Mood Whiplash: The final episode's plot about deciding to go to the party takes a turn after they return where Bernard & Manny end up in an argument and Manny delivers a The Reason You Suck speech. Despite the rest of the episode still having comedic moments, it's still horrendously dark compared to the first half.
Seasonal Rot: Graham Linehan left after the first season, and while the show was still funny, it didn't reach the rapid-fire insanity and crude misanthropy of season 1note This is the guy who co-created Father Ted we're talking about nearly as often.