A friend at work was wondering about pigeons. They really seem to like CTA stations. In fact, at the Davis stop on the Purple Line there are razor-sharp points jutting out from nearly every surface where a pigeon might alight.
At the Howard station, there are some similar pigeon prevention tools, but apparently not enough to keep them off the trains.
My work friend says they tend to congregate on the platform near the first Red Line cars on the trains heading south. She has seen pigeons waddle on the train, and personally shooed them off. Other times she has noticed them take off aboard the train. Then what happens.
A motorman told me if someone alerts him via the call button, he'll chase the pigeons off at Jarvis if they can't produce a transit card.
Another friend told me of the time she was waiting behind a person at Morse, waiting for the doors to open on the southbound train. When they did, the person in front of her screamed and ran down to the next car. Waddling around in the car was pigeon. My friend showed him the way off at Morse.