I am sorry to learn of this situation.
It really depends on what your coop agreement is with regard to the garage fee.
In many cases, the garage rent/rights are separate from the coop itself. This means that you may be obligated to pay for 3 months rent on the garage, even if you are not living in the unit for the full time, simply because you were living there for a portion of the time.
But the only way to determine your rights as to whether or not you owe these fees is to get the coop papers with regard to the garage agreement itself, and review them.
The Coop cannot charge you for anything that isn't written into the agreement.
You are liable for fees you incur under the agreement. (This would include late fees, unless you are able to negotiate them away).
If you do not have a copy of the agreement, ask them for one. Keep your communications in writing, it can protect you in the future, and help avoid misunderstandings and miscommunications now.