For me, the first problem was that the referee on the pitch was too much of a pussy to make a single decision for himself. The moment that first VAR call came to overrule his initial judgement was the moment that he decided to second guess every decision he made. It made the first half brick to watch, compounded by the fact that both he and the numpty in the office were incapable of interpreting the laws.
1) When was the first foul on the Lamela goal? For me it was the initial shirt pull on Llorente.
2) Son's pen was ruled out immediately by the ref, not VAR. Son however did not feint in shooting, only in running so again, the ref either interpets the law incorrectly or doesn't know it.
The second half was better, presumably at the behest of the FA or the managers, because it ran smoother then.