Yes, that can be a problem. I remember a topic on this forum that used a filter to alter the query where clause to correct this, but I don’t remember what the solution is. I tried doing a search of the forum without much luck.
There is another solution but not sure you want to try it. I have created a plugin that will convert fields like these, that is arrays stored as serialized arrays, into standard WP meta fields that use multiple database entries. Then instead of searching the ACF field with multiple like meta queries you can search the new field using
'IN' and supply an array. I thinks it’s working, and I’d love for someone to test it out and tell me if there are any bugs. https://github.com/Hube2/custom-field-converter
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