One of the big problems with the DMCA and a lot of similar laws is that they have no built-in protections for abuse. Anyone is allowed to claim anything and because of legal fears, many content hosts immediately side with the alleged copyright holder when there is no proof whatsoever. The only way I can see this not being a problem (other than a repeal of the DMCA itself) is if such actions start to have consequences.

Bot or not, this is an intentional action by Qualcomm. Github should push back against this if it wants to remain credible in the open source community. Are there some general provisions in the law that allow it to respond to abuse (which this is a clear case of) with their own lawsuit?

Of course, the Qualcomm repository should be pulled. Permanently.