It's definitely a sizing issue but it's more than that. I've tested it on 1080p and 4k. On some devices it works and on others it doesn't. Not sure why. Maybe as I get more familiar with Twine/Sugarcube I'll be able to make it work on more devices.well if you need more infos, just tell me what ya need and i will help out anytime ^^.
that being said, i play a lot of HTML games and i rarely come up with overlay issues
since you tested it on 1080p, maybe it is a resize problem?