Star, it appears that they are sewn together correctly, individually they look great!!! I think something happened differently when you made the black hex's.
First I would measure the height of both of these hexs...it appears that the black ones are narrower/shorter than the rest. Verify that your original sets of strips were the same width/height
Next I would check your seam allowances on both.
Pressing/not pressing can make a difference too... If you don't press inbetween additions the hex's can shrink, just like if you don't press them open fully enough...
I think if you don't correct this problem now, it will cause you a lot of problems when you go to sew the strips to each other.... mine had minor variances and I have a little rippling going on...but with a variance like this, I am afraid that it will become a much bigger problem...
There really isn't a way to trim down your other hex's to match the black ones, without taking away the kaleidoscope effect... (((HUGS))) I wish that I could offer nicer news than ripping and fixing these.... :( :( :(