When you configure a Weapon Action on a Homebrew Feat, proficiency with that action seems to be driven by the martial arts option, rather than the proficiency option.  The two should be independent.

Steps to reproduce:

• Create a new Homebrew Feat
• Create a new Action for that Feat
• Set up basics sufficient to make it appear in a character's list of Attacks, e.g:
  • Action Type: Weapon
  • Ability Score Type: DEX
  • Attack Range: Melee
  • Dice Count: 1
  • Die Type: d10
  • Damage Type: Slashing
  • Display as Attack: Yes
  • Activation Type: Action

Bug 1

• Select "Is Proficient" and deselect "Affected by Martial Arts"
• Save the Action
• Re-edit the Action

Observed behaviour:  "Is Proficient" is unselected
Expected behaviour:  "Is Proficient" is selected

Bug 2

• Deselect "Is Proficient" and Select "Affected by Martial Arts"
• Save the Action
• Re-edit the Action

Observed behaviour:  "Is Proficient" is selected
Expected behaviour:  "Is Proficient" is unselected

Other

• Create a new monk character
• Grant the character this feat
• Observe in the Action section that the Homebrew Action has both martial arts and proficiency on this Attack, or neither applied, dependant solely on whether "Affected by Martial Arts" was selected when configuring the Action (and ignoring "Is Proficient").

Thank you for the report! The team is aware of a bug where the "Is Proficient" checkbox automatically changes without user input. I am happy to pass along the additional information you have provided. :)