breqn is not yet stable (at least it does not have a version 1 yet). You might want to report that problem to https://github.com/wspr/breqn/issues
Here some quote from their documentation:
As it pushes the envelope of what is possible within the context of
LaTeX2ε, the breqn package will tend to break other packages when used
in combination with them, or to fail itself, when there are any areas
of internal overlap; successful use may in some cases depend on
package loading order.
The last statement is not true for your case. In the meanwhile, you should not use this package or switch from
tikz-cd which I would recommend in general.
This could look like the following:
% arara: xelatex
Your commutative diagramm goes here:
And your super long formula here:
If you cannot live without those two packages, you might generate your commutative diagrams externally (
standalone class) and include them as PDF. Or you tell us, what features of
breqn you actually do need. Maybe, one can take out that feature manually from the package implementation.