once it is quilted you will never see that joint- and remember- all applique has pieces (come together) yours is as normal as anyone elses- finish it up- quilt it- it will be ok=
one of the big uses for design walls is so you can put your work up and then step back- if you can not see something from 10-12 feet away- it is not going to be noticable when it's all done....sometimes we are just too (up-close)
relax and continue on- you are doing fine