Yes, they did have fit issues. I went through 2 Toyota brand hard tonneaus and both rubbed paint off of the front rail of the bed. Then I tried a completely different brand, Raider LoRider and it was garbage. The front was wide open (by design) on it so water would just flow in like crazy.
I ended up going with a soft cover, the Extang Trifecta. I couldn't be happier! In fact, I'm glad it didn't work out with the hard cover.
Here are some threads you may find helpful...
Hard tonneau and bed liner installed - pics
Raider LoRider installed - pics and impressions
Extang Trifecta installed - pics