Hi there,
I see that there is currently an open issue related to the Product Attribute filter in version 4.4+ of WooCommerce. It appears there was a possible fix that would have come out in 4.5, but it does not seem to have worked for several users so I’m not sure it was included. The issue description is a bit different (filters not displaying at all, rather than just leaving out some attributes), however if the filters you are using are the built-in WooCommerce nav filters, then the issue you are seeing could possibly be related to the report here:
https://github.com/woocommerce/woocommerce/issues/27419
That said though, I see that the display/behavior of the filters on your page are different from the default filters as well.
Default:
Link to image: https://d.pr/i/Q3nx6X
Your filters:
Link to image: https://d.pr/i/P7t1sU
The issue you are seeing could be coming from a conflict with code in the plugin/theme that is changing that filter display/behavior. I would recommend doing a conflict test to narrow down what is causing that, and check to see if you still have the same issue with just WooCommerce active when using the default Storefront theme. We have a guide for conflict testing here:
https://docs.woocommerce.com/document/how-to-test-for-conflicts/
To avoid affecting your customers, you may want to do this on a test/staging site. If you don’t have one already, your hosting company might offer one as part of your package. Alternatively, you can use a free plugin like https://www.ads-software.com/plugins/wp-staging/