Why would the breaker be tripping after removing a ceiling fan?
It sounds like you capped 2 whites together, which would be logical.

However, you've probably discovered a situation where one of the whites is a switched hot, improperly labeled (i.e. not labeled).

Try putting a cap on each wire by itself.

It's unlikely that putting a break in a circuit would cause a trip.  It's the opposite problem, a short that causes a trip.