hard to say until and unless we dont know your worflow...
We need steps to replicate the issue at our end,,,,
Sorry pretty new to this, here's what I did:
Opened a web doc in InDesign
Added another master page
Used the rectangle frame tool 6x
Made the frames interactive buttons and set the fitting setting to auto fit
Placed pictures into frames
Then inserted 6 pages after the second master page
And that's when the buttons stopped being clickable and became part of the background
The reason being the master page item are neither selectable nor Editable on the page.....you have to "override the master page item",
Select the page and then go to Flyout menu of the pages panel
Click "Override all master page item"
Not sure when you said the Button layer disappeared....