FWIW, as of today, running the latest + contrib, the FileManager plugin causes this to occur upon both shutdown and disabling the plugin via the Plugins interface. (64-bit multilib Gentoo, wxWidgets 3.0)
Removing FileManager.zip from /usr/share/codeblocks allows Code::Blocks to exit properly.
I get these errors only sporadic or better sometimes it happens on every close of C::B and sometimes not.
Enabling and disabling of FileManager has no such effect (at the moment), neither on C::B with wx2.8 nor on C::B with wx3.x from trunk.