I’ve managed to “solve” this issue.
The most probable cause is using revisions in the content type which uses repeater field (it was the cause in my case).
The easiest workaround is to remove support for revisions and remove all revisions. Less naive approach is modifying SQL query and eliminate revisions (it should be mentioned in the official guide https://www.advancedcustomfields.com/resources/querying-the-database-for-repeater-sub-field-values/).
Here is how it should be handled, see 4th example on this page: https://www.advancedcustomfields.com/resources/query-posts-custom-fields/
