Guessing based upon video from comments: https://i.imgur.com/T55Fihx.mp4
If the green/yellow shapes are comprised of a bunch of little, individual, pieces ....
The negative offset in the pattern editor may be failing to replicate these individual pieces because they fall outside the pattern tile clipping area.
To correct this....
- Select all the green and choose
Object > Compound Path > Make.
- Then do the same for the yellow.
Now create your pattern the same way you have.
By creating compound shapes of all the pieces, Illustrator sees the pieces as one, singular, object rather than a bunch of pieces. This means the shape won't be "clipped" as long as a part of it is within the pattern's tile.