Usually each puppy is crate trained separately. Often this is due to adult dog size or concerns about interdog aggression while unsupervised. You have not done anything wrong by keeping them together--it sounds like it has worked great for a year!
The first thing I would do is take your dog to the veterinarian for an exam and a urinalysis to rule out any medical cause for inappropriate urination. If there is no medical reason then we are left with behavior. Around 1-2 years is when puppies reach full adulthood, this can be a time when the dominance hierarchy is established or changed. Make sure you have identified which dog is inappropriately urinating--most likely it is the submissive dog. In that case separating the dogs may solve the problem. Also look for any other environmental changes, changes to the routine or stress that may be causing this abnormal behavior.
Good luck!
The first thing I would do is take your dog to the veterinarian for an exam and a urinalysis to rule out any medical cause for inappropriate urination. If there is no medical reason then we are left with behavior. Around 1-2 years is when puppies reach full adulthood, this can be a time when the dominance hierarchy is established or changed. Make sure you have identified which dog is inappropriately urinating--most likely it is the submissive dog. In that case separating the dogs may solve the problem. Also look for any other environmental changes, changes to the routine or stress that may be causing this abnormal behavior.
Good luck!