Ah yes, this has been reported before. It's not clear why it's happening, but I think I know how to fix it (So I'll be patching it soon.) Typical of course that I can't reproduce it on my saves at all. If you know how to enable the console in Ren'Py, you can do that and then run the commands below. (Exactly as written. Case sensitive. Do it while the phone is open and the messages should pop up)
hide screen AkemiMessages
show screen AkemiMessages