They all get like that..I use a thin bead of clear silicone chalk,just below the rubber line [ where it meets the winshield-you do not see it once assembled] It will peel off if you have to do the filters again.
If the channel is not broken, you take a thin blade and clear the slot out so that the rubber lip will go into the channel.. it will not snap in there if the channel is not clean/clear.
It is not that important..check the corner drains I put the garden hose right down in them while I have it apart.