I doubt that there is any bank charging $50 for a single bounced check. $30 or less is a more likely fee.
If he is trying to get you to pay for fees he is charged because he wrote checks against your check before it went through, that is his problem. People should not write checks against funds that have not cleared.
Many banks, if they see a check with a date 6 months or more before the date of cashing the check, would refuse to cash the check. Occasionally, the persons handling the checks may miss and allow a check written 6 or more months ago to go through.
Holding onto a check for 3 months is not all that unusual.
On another hand, many companies specify on their checks that the checks are good only for a certain number of days (such as 60 or 90 days).
Unless you have an agreement with him to pay his bounced check fees, he may not be successful in getting a court to order you to pay the fees.
If you are going to fault him for not cashing the check soon enough, you may have to fault yourself for not being aware of which checks have not cleared your account.
The dispute seems to be at most about $50 since you are not disputing that you would pay the original amount. You may want to ask him for the amount he is charged solely for your check being returned and then split the difference with him on that amount. Taking each other to court for $50 may not be a good use of resources for either of you.