I don't know about the merits of what happened; but I think it was wrong of Bestmark to stop payment the checks after they were issued. In doing so, they not only denied the payment, which may have been their right, but they also cost the shopper bank fees, which was not their right.
In my opinion, if you discover after you have paid someone that the payment was an error, your recourse is to ask for it back, and if it is not given back voluntarily, then you need to take them to court. You don't "steal back" what you think was stolen from you.
A stop payment or bounced check has a domino effect: OP incurred fees for the stopped checks. OP may have written checks against that money, which then bounced when the stop payment occurred, incurring NSF fees as well. The people OP wrote checks to may have written checks against that money, and those checks might have bounced, causing those people NSF fees.
So BestMark may have caused innocent people three or more times (depending on how many checks bounced) the $400 they wanted back, just because their internal processes were insufficient to prevent the payments going out erroneously. They did not have the right to cause all that trouble, regardless of what OP did to cause it. That's what courts are for.
BestMark should have made their case in court. The harm they caused others is not justified by the money they felt OP owed them back.
Time to build a bigger bridge.