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.
Esoteric Happy Ending: Some viewers have a very dark interpretation of Vanessa's future relationship with Juno's son and where it might lead. Though the movie paints her in a sympathetic light for choosing to go ahead with the adoption after Mark leaves, one can't help but wonder how she'll cope with being a single parent while still reeling from her painful split with Mark.
Genius Bonus: While the movie mentions that Juno's named after the Roman goddess Juno, it doesn't mention that one of the main domains of the goddess is childbirth.
Mark and Juno in general. More than one viewer might have thought this movie was about to take a turn into much creepier adulterous May-December Romance territory with the way Mark kept being so friendly to Juno and the way she kept spending time alone with him, but no, that's not what happens.