Why did I get wrinkled bagels? I made bagels for the first time yesterday. I followed the instructions...my bagels tasted great...but they ended up &quot;wrinkled&quot; after baking. It was a copycat recipe for Panera cinnamon crunch bagels. It may be possible that I didn't boil them correctly, it called for 45 seconds on each side, but I didn't have a timer and kept losing count with family interupting constantly. It only called for &quot;flour&quot; and I used some bread flour and some all-purpose. It didn't call for rising after shaping, only letting it rest 10 minutes. Any ideas?
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)