This issue can occur if you are using a custom filter condition along with advanced filtering, and have grouping parentheses. To fix this issue, make sure there are no spaces between the parentheses and the numbers.
For example, the following Custom Filter Condition is incorrect:
(3 OR 4 OR 5 ) AND 6
The space between the 5 and the right parentheses will cause the 6th filter to be ignored. The above example should look like this:
(3 OR 4 OR 5) AND 6