Facet filters display the values returned in the search results. When "Show products instead of variants" is enabled, Algolia uses deduplication/grouping (distinct) so that only one variant is returned for products that share the same product ID.
As a result, the facet filters will reflect the attribute values of the variant that was actually returned in the search results, rather than the values from all variants associated with that product.
As the Algolia Shopify app doesn't provide a separate "facetingBeforeDistinct" setting, you can set the "faceintAfterDistinct:false" parameter using the InstantSearch Custom hook.
For further information on how to set "faceintAfterDistinct:false", please review this Support article:
https://support.algolia.com/hc/en-us/articles/32015058751505--Shopify-How-can-I-change-facetingAfterDistinct-to-be-false