For the sake of testing, can you create a copy of your toc and move those topics into some sub-folders to see if it still does it when the list is shorter (and maybe determine how many topics it takes to cause the overlap)?
If you also post which version of Rohohelp, which output and which skin/template you're using, I can have a look to see what I can see.
But I suspect for a proper fix it will need to be taken up with Adobe either support for an immediate answer, or via a bug report for assessment for a later release.
See the following page for support contact options. The email address is recommended as it goes to a dedicated Robohelp team.
There are longer lists of topics, but RoboHelp never had this output problem with the TOC in previous versions. Is there a way that I can get the actual RoboHelp file to you with the template? I don't think there's a way to do that here. I'm not getting any response from the Bug reporting link. There have been cases open since September.
If you want to talk to RH support folks, use https://helpx.adobe.com/contact/enterprise-support.other.html#robohelp for your Adobe Support options. I'd recommend using the tcssup@adobe.com e-mail address as it reaches a team dedicated to Technical Communication Suite products including RoboHelp.