You don't have your threads setup right with the Net::SSH2 object. Threads are a tricky business, and you can't just throw code into thread code blocks and expect it to work, especially when modules(especially complex networking types) are thrown into the soup.

Threads get copies of the parent when spawned, and some objects are not thread safe.

But from your errors, you may just need to manually close the SSH2 object, before thread destruction. As always, show some code.