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Do your footprints have a keep-out layer drawn like a courtyard?
I expect that multiple footprints are overlapping on those keep-out layers.
These layers may be hidden, obscuring the problem.
in the table, there is explained what to check - what layers and what components. try to have a look at them, looks like there will be something what needs to be adjusted.
Especially: Shape "Package Keepout / All" ... that may need a special attention.
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