What version of Hugo are you using (hugo version)?

$ hugo version
Hugo Static Site Generator v0.68.3/extended linux/amd64 BuildDate: unknown

Does this issue reproduce with the latest release?

Yes, CI pipeline is running

$ hugo version
Hugo Static Site Generator v0.69.0-4205844B/extended linux/amd64 BuildDate: 2020-04-10T09:16:58Z

Expected Behavior

https://blog.ctmartin.me/amp/[section]/
https://blog.ctmartin.me/amp/tags/
https://blog.ctmartin.me/amp/tags/[tag]/

Actual Behavior

https://blog.ctmartin.me/[section]/amp/
https://blog.ctmartin.me/tags/amp/
https://blog.ctmartin.me/tags/[tag]/amp/

Misc.

This may be similar to #5760

Code: https://github.com/ct-martin/blog.ctmartin.me (note that theme is a git submodule)