So sorry! Any opening larger than 1/2" diameter needs to be closed, and are there tunnels into the pen from underneath?
Only poison bait will get them all!!! Set out bait stations that only rodents can enter, check them daily, and put any dead rodents in the garbage, not outside. You need to change the bait type every week or ten days too. Inside the coop, a bait station inside a closed live trap will be accessible only to the rodents, not to the chicks.
I lost eggs and three nice pullets to rats last year, and had to fix everything, and use bait.
Mary