When Jalapeno Peppers are beginning to wrinkle on the skin it's a sign that the Jalapeno Peppers are going bad.
However even when the Jalapeno Peppers are just a bit wrinkled they can still be safe to eat as long as the Jalapeno Peppers do not have a bad smell to them or the color hasn't changed to a brown or other color other than red.
Red colored peppers usually means the peppers have gotten hotter but if the Jalapeno peppers turn other colors such as brown or possibly grey then they are usually bad and should be thrown out.
The Jalapeno Peppers when bad will usually have a bad smell to them or at least an off smell to them along with the wrinkles.
If the Jalapeno Smells okay and is wrinkled then it's safe to eat as wrinkled Jalapenos does not always mean they are bad but it is a sign that they are going bad.
Jalapenos should last for a few weeks in the refrigerator or at room temperature and sometimes longer but usually after a month they are going bad and usually need to be thrown out.