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Apple Pay payments aren't logging
Open Ctrl Log, go to Settings, then Apple Pay automation. It shows the last payment it logged and has a test button. If the test works but payments don't, check that the automation in the Shortcuts app is turned on and set to run immediately.
Something logged in the wrong category
Tap the entry and pick the right one. The next payment at that store goes to the category you picked.
Getting your data out
Settings, then Export data to CSV. It works whether or not you pay for anything.