I actually suspect that Tony Brothers (the official who called the foul) probably was reluctant to call a flagrant on the play in Miami last night because of the controversy about the call on Manu the night before.
As to the Manu call: I think it was such an odd situation because at the moment of the call, neither Bill Kennedy nor Bill Spooner (the two officials who were closest to the play when it occurred; Kennedy was in front of the Spurs bench and about even with the play and Spooner was on the other sideline and slightly behind it) indicated a flagrant foul instantly. For Javie's rationalization of the call being correct without Allen's theatrics, it sure looked to me like Spooner (who was first to the play) saw the aftermath and then looked to Kennedy with the idea that it might be called a flagrant. Foster (the crew chief) was trailing the entire play and approached the others and decided to review. My understanding of the replay rules is that they can look at the replay only if they call it a flagrant on the floor; it seemed almost like Spooner and Kennedy weren't sure and decided to call it a flagrant to allow review.
Once they did that, however, the burden for changing the call required clear and conclusive proof that the play was not a flagrant foul and, as Javie's analysis suggests, that burden was not going to be met with that video, which meant that the call -- by letter of the law -- had to stand.
I think it suggests that the league should change the replay rules (again, my bad if I've misunderstood them) to permit the play to be called a common foul and give officials discretion in limited late game situations to look at video to confirm that call with the burden being greater to upgrade the foul than to downgrade it. But if you want to have a fairly objective reason for the difference in the calls, I think it lies in the standards for going to replay on flagrant fouls and the burdens that must be met to reverse calls by replay.

