That particular situation that happened between the both of you may have been what initially planted the seed of doubt in her mind about her relationship with you and the prospect of becoming exclusive.
Prior to the week in which the both of you didn’t speak, you felt as though she had been showing signs of wanting to be in an exclusive relationship.
Perhaps, the situation that later occurred punctured whatever fantasy she may have concocted about what life with you as an exclusive boyfriend would be like.
After the night that the both of you made up, she may have spent more alone time thinking about the situation that occurred. This may have actually been what put her in a bad mood, leading her to seek solace from friends to no avail.
It may be helpful to ask her if she still has issues about that situation and if so, what they may be. Perhaps try doing this before suggesting a temporary break.
If indeed the source of her continuous flaking stems from this situation, clearing it up further with her may help to mend the rift that has developed between the both of you.
However, if she tells you that she has no lingering issues in reference to the situation, you can then go ahead and ask her if she would like to take a temporary break from the friends with benefits relationship.