It's okay to enforce a late fee
I don't know who needs to hear this, but if your lease says there's a late fee and your tenant is late...then there's a fee. It's okay. It's what both parties agreed to in writing in a contract. The story doesn't matter. The tenant's attitude about it doesn't matter. You hold up your end of the lease when they need you to. When you get that emergency repair phone call at 2am on Thanksgiving day for example, you handle it. That's the deal. If you feel like you need permission to enforce your lease, then consider it granted.