Stellaris updates so often that mod authors often don't bother to update the version number even when that is all that needs to change. So here's a guide to doing that on your own. From my experiments, it looks like steam does not actually update mod files unless you unsub or the mod author makes an update of some kind, so you should only need to do this when you unsub, or Stellaris or the mod are updated. Remember that mods can be updated fairly often if it's an active author. Authors will often post a link to another mod and leave one or the other for legacy so watch for that as well. Moving on!

Now, how do you fix this? Start by going to the mod workshop page. The URL for the page has the number steam uses to identify the mod at the end of it. You will need this number.
Now you need to go to:
C:\Users\<your user profile name>\Documents\Paradox Interactive\Stellaris\mod.
In this folder you will find a whole bunch of .mod files. These are really just txt files, so you can open them with any old text editor. Remember that number I had you find? Here is where you need it. ugc_<mod id number>.mod. You need to open the file with the id number of the mod you want to change.

Almost there! Now in the file you just opened, you will find a line that looks like this:
supported_version = "2.3.1"
All you have to do from here is change the version number to your current version. Whatever that is. To save a bit of time between minor updates, you can replace the patch number (MAJOR.MINOR.PATCH) with an asterisk (*). E.g. 2.3.*
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Save that ♥♥♥♥♥, and you're done! Have fun purging those xenos!