One is App Store distribution. The per install license thing is bullshit but it might comply with the law. Keep in mind the DMA was written to privilege companies like Spotify, not to give you a property right to install whatever you want on your own device.
The other issue, which deals with a different DMA rule, is that Apple can’t privilege WebKit over other rendering engines. That means PWAs have to be able to run in any rendering engine installed.
To make that work, they’d have to build out APIs to allow third party rendering engines to do all that WebKit does to render PWAs. Or they could disable PWAs altogether and then nothing is privileged.
Seems like a case study in unintended consequences. If the EU has consulted with anyone who understands technology, this could have been explained beforehand. Or maybe it was. Either way, the WebKit issue might be lazy compliance but it doesn’t strike me as malicious.