I cannot find the direct meaning of this phrase online.
What does "no vaya a ser que" mean?
No vaya a ser en este contexto es como una probabilidad de que suceda algo por lo que se vaya a hacer.
- No voy a molestar al perro, no vaya a ser que me muerda
[I am not going to bother the dog, because it could bite me]
No voy a dormirme tarde, no vaya a ser que llegue tarde mañana a la escuela.
- [ I am not going to sleep late, because I could wake up late tomorrow for the school]
No vaya a ser in those contexts is a kind of probability some happens if you do do something.
Please correct me the mistakes in English.
Vaya is also the conjugation of imperative of ir as in "Don´t (you) be ......" It could be as Jubilado said or something quite different like Francot says about some thing, or even a wish that something not happen. In the end this is just some words in a clause and no context, so alone it means nothing.
Literally it means "It's not going to be that..." The verb vaya is the subjunctive form of va. There is something preceding the phrase that requires the subjunctive to follow. Perhaps you have a larger context which will explain the meaning further.
Even though the best answer has been selected and rightly so. I am bumping it up because I think it is a good learning post. Essentially what I gather is that it means "because" in the sense of a logical (but not desired) consequence of a preceding act. It seems to have the nuance of the English word "lest" though perhaps used more frequently. And it is a phrase that itself is followed by the subjunctive.
The native speaker Francot has done us a great service in his answer. If you are reading this post of mine please vote for him when you are done. We want him to help us more in the future and if he needs help in English we are here for him!