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:

 1. Lugia
 2. Articuno
 3. Moltres
 4. Zapdos
 5. Raikou
 6. Entei
 7. Suicune
 8. 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 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.