Is this the area you're talking about?
View attachment 122363
I can think of three options, off hand.
1 - Live with it.
2 - Fabricate a piece to cover the area.
3 - Buy different liners.
Personally, I have no intention of doing anything about this gap. We have Hook Roade flares on both Jeeps. Mine has the liners, hers does not. Why does mine have them? Because when I ordered the parts for the build, the flare-only package was out of stock. We've driven her Jeep through water many times. No problem. I think the inners are more cosmetic than functional.