Hi Jenni,
Sorry you are having issues with your Flow Frames. I’m not sure in which way they are not lining up - photos would help as the others have mentioned.
They do not line up horizontally - they are designed with offset heights to help the caps stay intact when harvesting.
They also have little gaps so that the bees can fill them with wax, and this allows the cells to be split.
Here is a nice photo which shows what the bees have to do first before the bees can start to fill with honey:
This topic is good to read to encourage bees to take to the frames:
To reset the frames, you can see how to do that here, with info, photos and videos:
Fixing bent/misaligned Flow Frames here:
https://www.honeyflow.com/faqs/all/fixing-bent-misaligned-complete-flow-frame-re-assembly/p/180
If you have any trouble doing any of the above, just email customer support with some photos and your order number and my colleagues who work in Flow Frame troubleshooting will be able to help you further 