Thats a bug. Just restart the level and try again. Also spam click on a box until it shows the out line. (You can also only join two boxes before you have to join two more, if you didn't already know this.) Anyways, thanks for the feedback
I went back to the game and I figured out what I was doing wrong! I wasn't hitting enter after making a pair. I'm a dummy and didn't realize you needed to do that between pairs haha. I went back and played through it and enjoyed it a lot more. Great game and fun mechanic!