I don’t think so, if you can’t disable the acf plugin that’s bundled in the other plugin then I’d contact the author and see if they have a way to do so. On the other hand, the other plugin may not work 100% correctly with the new version of ACF. At any rate, you should talk to the author of the other plugin to find out.
More than likely the problem was caused because the version of the plugin bundled in the other plugin was actually loading before the stand alone version.
