First, reach out to your supplier and explain the situation to them. A lot of times a good supplier will make an exception and allow you to place the order especially if you are relatively close to the MOQ.
A different option is making up the difference using another product you can sell. So, if the supplier is making you buy 250 units of item A but Amazon will only allow you to send in 200, explain that you will purchase 50 units of item B in order to make up the difference and meet the MOQ (assuming item B is a profitable product). You could also buy 25 units of item B and 25 units of item C to make up the difference and diversify you purchase.
Additionally, you could have a part of your shipment sent to your location or a 3rd party prep center for holding until Amazon permits you to send the rest of you shipment in. The problem with this is there is no set time for how long Amazon will make you wait to send in the rest of you inventory (although if you sell through your product quickly then the time frame should not be that long). The longer you have inventory, the greater risk of the listing to change by potentially dropping in price, more competition, and worse sales rank. However, if it seems like a stable product, everything on the listing looks good throughout the history (price, competition, BSR), and the extra shipping cost to you and then to Amazon is not an issue, then this could be a good route.
Amazon won't let me send in my shipment, and my supplier won't let me buy less.
I met my distributor's MOQ, now Amazon is telling me it's too much to send in.
