If that's the case, it must have changed at some point. Lastpass and Duo both support multiple U2F keys, and have for at least a couple of years. I have two keys registered with Duo for login at my school and also through Lastpass's non-Duo U2F support.

My college uses Duo and it has no such restriction, if you tried this recently and couldn't add more than 1, it is probably set by LastPass/1Password.