Changes occur when a filter is applied, but’s that’s not where the rules for the alteration originate from.
Either your theme or a plugin you are using must be hooking into that filter and be adding a callback function/method, that is responsible for the $categories
array being emptied.
Deactivate all plugins, switch to a standard theme. Things should be back to normal. Reactivate everything one by one and find the culprit.
Alternatively,
cd /path/to/wordpress/wp-content/plugins/ && grep -r 'get_the_categories' .
from a *nix shell should also help you find it.
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