Yeah, I've received a few reports of the game flagging anti-virus software. It's due to the .exe being compiled with GameMaker without a code signed certificate. I ran the file through Virustotal and it shows that there aren't any issues. Still frustrating though since the only solution to this apparently not happening is to pay security certifiers like $400 for a certificate which stops it from happening. I'll likely do that down the line once the project is generating enough support to make that investment make sense. As for the specific things about clipboards and keystrokes, it's just that GameMaker's runtime contains code for all GML (the language) functions which include things like clipboard capability.
There's nothing in the program that sends me or anyone any data or connects to any network and there are no registry or external calls. It's sandboxed to it's own save folder. Nothing malicious in the code. Sorry for the scare, though, it is annoying!