I think he gets undue flack from people desperate to see Messi win an international trophy. That said, when he was with Madrid I recall him fluffing chances when it mattered the most.
Whether it's undue or not, it's entirely understandable given the circumstances of his misses in those finals.
Obviously Messi fans will have an agenda, but looking at it objectively it's an unfortunate recurring trend that for once does seem to merit the description of "bottling it".
2014 WC Final : early on in the game he is gifted the ball by a bad backpass from Kroos, 1v1 he panics and rushes his shot which was admittedly not easy as it was a volley, but still... pretty terrible to fire it wide by such a distance in the end.
2015 CA Final : final minute of regular time and he can't put it away -- this one I don't even blame him at all, it was Lavezzi's overhit pass that fcked that move up completely, in my opinion anyone who blames him for this has an agenda. That said, he still failed in a decisive moment, being the first one to miss in the penalty shoot-out at 2-1. Sure, penalty misses happen to everyone of course, but put together with the rest it's easy to see why he's called a bottler.
2016 CA Final : again early on in the game, again he's gifted the ball by a defender and can run 1v1, he doesn't completely round Bravo and tries to dink it only for it to go just wide... easily the worst flop of the 3 instances, considering he was coming off the best season of his career and that he had scored 4 goals in the previous two rounds against Venezuela and the US.
It's not that just that he missed great chances, it's that he literally missed two complete gifts from the opponent early on in two major finals, both times 1v1s where he was in total control but somehow can't even hit the target from such an advantageous position...