Why did I get wrinkled bagels?
It sounds to me like you've already diagnosed the problem. Just to cover the basics, though, here's some of the reasons why bagels are unsightly, based on my personal experience making bagels and a few internet resources (links below):

Failure to knead the dough adequately, leading to inadequate gluten development.
Overhandling of the dough while shaping the bagels.
Inadequate proofing after shaping.
Putting them into a roiling boil instead of simmering water.
Leaving them to get cold after boiling before baking -- they need to go into the oven still warm from the pot.
Making them during Passover*.

Per your description, inadequate proofing was certainly one of the reasons your bagels were lumpy.  You may have been affected by the other reasons as well.
Resources:

Smooth bagel recipe
Bagel Troubleshooting
Reddit Q on wrinkly bagels

(* the bit about Passover is a joke.  However, I did once make the mistake of making bagels during Passover, a Jewish holiday during with you don't make or eat leavened bread, and they were lumpy and flat, so maybe check the calendar just in case)