Another possibility is that they are using naive port-based filters in their traffic shaping rules, and it thinks that any encrypted-looking packets not destined to one of a white-listed set of ports is torrent or other P2P traffic.
If you run the server side of the VPN as well as the client, you can test that possibility by trying other known ports (1194 that OpenVPN usually lives on, 433 if that isn't already directed elsewhere on the target address, ...).
To copy and paste another reply I just made:
"I ran some tests with the guys in WireGuard IRC which seemed to confirm that the issue is specifically EE limiting UDP whether by QoS or otherwise."
I'll give OpenVPN a go over TCP once I have a chance to set it up and I might even consider contacting EE for info.
I would mind the fact that it limits my throughout to, at best 12Mb down, but when on WG it typically approaches 0 making my device unusable and I've already ruled out the rest of my network.