Should I use my official legal name or the one I'm known by on my Master's dissertation? My official, legal name is A, but I'm know by most people as B. B relates to A as Bob to Robert, however this connection is only obvious in my country of origin where I am no longer based. I am known primarily as B, among my friends and colleagues. In order to build a consistent professional profile over the past several years I've been making a conscious effort to not use A at all, as I've noticed it causes some confusion. My undergraduate degree certificates have my legal name on them but I feel like in a Masters I am currently writing up I would like to proceed with "migrating" over to being a "full-time B". I am not sure though if that in itself won't generate damaging inconsistencies in my professional profile / online presence etc, with various certificates awarded under different names.

Should I use my official legal name or the one I'm known by on my Master's dissertation? What kind of problems can I expect from going either way?
You could write your name as Robert "Bob" KubaFYI, if your university policy allows for it. At least in the US, that's a standard stylization to indicate a nickname or unofficial name one goes by regularly. Classmates of mine who were international students from Eastern Asia and had traditional legal names but went by English names commonly did this.