I had better confirm how you've done this before I try to replicate the issue myself.
You have one normal custom search View which has a filter for some custom field, meaning it will add a URL parameter when applied, something like ?wpv-wpcf-field=foo
You have a second View on the same page. It doesn't include any filter controls, but you have added a Query Filter which is the same as that in the first View, which filters based on the same custom field and where the value comes from the same wpv-wpcf-field URL parameter.
I couldn't reproduce the problem, so I suspect your set up is somewhat different.
Could I get credentials from you to take a look and see the issue in person?
I will mark your next reply as private so that I can get log-in credentials from you—you may want to create a temporary admin user for me to use that you can later delete. And be sure to have a current backup of your site, even though I don't intend to make any changes other than possibly to temporarily add a backup plugin to take a snapshot of the site.
Can you also confirm which are the Views in question, and where are they displayed?