Filtering Data with multiple checkboxes

I have a spreasheet that has multiple checkboxes in one cell. One of the columns is "Dept" and sometimes I just want to see one or two of the departments at a time or sometimes I just want to see a specific cycle year. When I use the filter option, some of the checkboxes tend to bundle up at the bottom of the spreadsheet. Is there a way to prevent that?

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I saw a post that said to change the format controls to dont move or size with cells so you wont get the overlapping issue but if I select that, then when I filter, the checkboxes for that specific row won't stay with the appropriate person