Depending on the app, the temporaries are cleaned when you close the document or when you fully exit the app. With exiting the app we mean really exiting the app completely – not just closing the document in this case. Notably Microsoft Office programs behave in this way. There may also be some issues with some Windows 10 store apps that do not exit even when you request them too, for example the image previewer does this sometimes.
If you are still having problems, please contact our support and include a screen shot of the AxCrypt main window when you have left-over files, as well as the files mentioned in step 2 here: https://www.axcrypt.net/blog/send-complete-error-report/ . (We do not at this point need the event log mentioned in step 3).