I've been running two computers with El Capitan and the current version of InDesign. I have no such problem.
Start by restoring your InDesign preferences:
What version of InDesign?
El Capitan version?
I have the latest version of both InDesign and El Capitan. I will try restoring the default preferences and see if that fixes the problem. Thanks to all for your responses.
Please disable auto-hiding the menu, If it's turned on. Please follow the steps below:
1. Launch System Preferences on your Mac with a click or two, then click on the General icon.
2. Next, click on the checkbox next to the awkwardly named “Automatically hide and show the menu bar” entry
3. Your menu bar will slide up into the top of your Mac’s screen immediately. You can quit System Preferences at this point.
Let me know if this helps.