In Cosmic Encounter, where do my ships go when I pull them from the warp if I already have 4 ships on each of my planets?
When returning ships to your bases, you may put the token(s) on any bases where you currently have tokens.

Four is just the starting number, not the limit. You can have more than four.

(Note some rulesets call bases "colonies" instead. It's the same thing -- it just refers to your ships on a planet.)