Thanks to Plums video, I figured out the issue with 2 nests up at once.

The nest order goes

1 - Lower NE nest (X)

2- Lower SE nest (Square)

3- Lower SW nest (Star)

4- Upper NE nest (X)

5- Upper SE nest (Square)

6- Middle nest (above boss)

7- Lower NE nest (X)

8- Lower SE nest (Square)

9- 2 NESTS! - Lower SW nest (Star)/Upper NE nest (X)

10- Upper SE nest (Square)

11- Middle nest (above boss)

12- Lower NE nest (X)

13- Lower SE nest (Square)

14- 2 NESTS! - Lower SW nest (Star)/Upper NE nest (X)

So "9" and "14" is the culprit of 2 nests.  Fortunately for us, we killed it shortly after 14 hit so we didnt drag it on horribly long.  So it looks like after 1 full rotation of lower then upper nests, they will overlap with the last lower and first upper nests at once to give it that "soft" enrage mechanic.