That's correct. You are filtering a single numeric field; when a user provides a number to filter by, the query looks for posts with a field that has that same value.
For partial matches you would use a text search field (and to include custom fields rather than just the post title and content in the search fields you would need to add Relevanssi to your site).
One option, to continue using a filter for the numeric field specifically, would be to use the API filter wpv_filter_query to modify the query arguments, to change the comparison from '=' to 'LIKE' (and wrap the filter value in % so that the generated query looks something like 'meta_value' LIKE "%999%" in your example).
