Applications that hook into the Window Manager are dangerous in general (it does so by injecting its code into Apple's system process). I'd be willing to bet that's what Popclip is doing, especially since they have an "excluder".
Up until 10.10, Dropbox had to do code injection on the Finder to work. They did it very, very, very well (employing lots of ex-Apple Finder engineers), they only tried to do one simple thing (adding the sync icons to your Dropbox folders), and it still could
occasionally cause Finder crashes. Code injection is
dangerous.
Also, shell extensions that do stuff to "windows" often interact badly with MC on Mac
and Windows. I have to exclude MC from the "button overlay" functions in
DisplayFusion on Windows, for example, or it does some crazy things.
Most of those applications are designed assuming applications use the standard OS window controls. But MC doesn't use
any standard OS widgets at all, which is why it can be cross platform, but it also isn't written against a publicly available "cross platform library" or system (like Java or whatever). JRiver wrote everything themselves, in pure C++, to be cross platform. So, it is a pretty weird case, and unless they built something special for it, it isn't surprising that it would freak things like that out.
Not saying Popclip is bad (I know
nothing about it). But, be aware that running things like that is dangerous, and can interfere with the way other applications behave. Now that you know you have it, keep an eye on it.