QSYS generates a second unneeded reset controller

I am having issues with my QSYS design and I figured out the issue is that one of my QSYS modules seem to have a different reset controller. The standard one looks like this:

https://www.alteraforum.com/forum/attachment.php?attachmentid=6751

The one that is connected to the single module looks like this:

https://www.alteraforum.com/forum/attachment.php?attachmentid=6752

What could the issue be?

Edit: Turns out there was a weird refresh problem, mods can delete this if they don't find it useful.