For example when using the BuildBuddy CLI, it suggests to add another line to your .bazelversion file: https://github.com/buildbuddy-io/buildbuddy/blob/2330dfa876525fb8a687b0510492c9eada6a63b6/docs/cli.md?plain=1#L51. In this case it will try to read the whole file and fail to parse.
Not sure how to handle the general case, I don't know of any other tools that do this (but maybe there are ones out there), but special-casing buildbuddy is an option. Apparently bazelisk supports fork/version as a parameter, but this is different it seems.
Pretty low severity, can easily work around it by setting the version in the extension.