Hi Joshua,
Is this something wrong with the way that I'm setting permissions
Honestly, almost certainly. When we get questions like this, the most common root cause is typically "permissions inheritance behaved (correctly) in a way I didn't expect it to". It's the old quote "The good news about computers is that they do what you tell them to do. The bad news is that they do what you tell them to do." in action.
Most places where you can set/view permissions have an "Effective Permissions" section that shows the calculated permissions for a user or group, and in some cases where exactly those permissions are coming from. I'd start there. If you think you'd benefit from some learning resources on Laserfiche repository permissions, I'd be happy to point you towards those.
You can also reach out to your Solution Provider and ask for a second pair of eyes.
I'm not aware of any open bugs with the Laserfiche software that would cause permissions to be set incorrectly in this manner. Though it's not impossible, the permissions model is extremely battle tested across the entire customer base and hasn't changed much in the last decade. Odds are 99.95%+ this is a configuration issue of some sort.
Cheers,
Sam