I have seen a couple like that. However, they are only on bikes that have had the swingarm, and or, boot removed for some reason. I suspect the dealer just tossed it in, and didn't get them right when reinstalling them. This can cause the plastic "holder/clip" to get distorted, and make it nearly impossible to get it reinstalled correctly later down the road.
The only two options I can see are to install it as is, and it will mostly seal, or replace the boot and clip with new.
Sorry, wish I could be more help.