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.
The legendary birds (Articuno, Moltres, Zapdos) were twice catchable. First a month per bird, then 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.