Can you please be more specific about the issue:
– Do you want to search WooCommerce products by ACF custom field values?
– ..or do you want to display ACF values somewhere?
– ..or is it something else?
In that case, make sure that these custom fields are selected for indexing on the index table options panel: https://i.imgur.com/I2lZ46I.png
After choosing the cusotm fields you need, and re-creating the index table, it should start working.
I think I have found the problem. I had to disable the Polylang compatibility option here: https://i.imgur.com/mp87vuu.png
I believe it was because there is only one language, and the products may not be assigned to any language yet. It should return them now correctly.