Built-in microphone level auto adjusts itself
If you haven’t already, try resetting the NVRAM and attempting to replicate the issue. Here’s an Apple support article on what an NVRAM resets does and how to do one.

https://support.apple.com/en-us/HT204063

If the issue continues, create a new user account and attempt to replicate the issue in that account. If the issue persists in a test user account than, I’d advise visiting an Apple Store for them to run audio diagnostics and determine if you are having a hardware issue or if your operating system needs to be reinstalled.The article below highlights creating another user.

https://support.apple.com/kb/PH25796?locale=en_US