There were multiple limited time Pokemon, all legendaries. It is currently not known if they will return (all of them or a select group). These Pokemon were:
- Lugia
- Articuno
- Moltres
- Zapdos
- Raikou
- Entei
- Suicune
- Ho-oh
Currently there is another legendary active, Groudon, so be sure to catch that one while it is still possible. Also Mewtwo is available through Ex-raids at this moment in time. Also, this weekend is the first time (and for now only) time to catch Delibird!
The legendary birds (Articuno, Moltres, Zapdos) were twice catchable. First a week per bird, then about another month where all 3 birds were available at the same time.
Another 'issue' might be the special hats for the Pikachu family. At specific moments in time they were catchable/hatchable with a different hat.
One other thing that might be annoying is that there are regional Pokemon. For example, Farfetch'd is limited to Asia only. However, there has been an event where it was catchable for 48 hours worldwide. You can still catch Farfetch'd in Asia, but not so soon in your hometown (if not located in Asia) though.