There are several Megas where Mega Evolving straight away may not be the smartest thing to do. Pinsir and Gyarados, for example, have Moxie as a normal ability. So if you are sure Pinsir can faint the opponent you might not mega-evolve it until you get the Attack boost.
Mawile can be switched in and out to make the most of Intimidate. Gengar loses its Ground immunity, and Pinsir becomes 4x weak to Stealth Rock, so you might choose to hold off for those reasons as well.
For some Pokemon there is no reason to wait, however. Blaziken and Medicham, for example do exactly the same things in their regular form as their mega does, but with better stats, so there is no reason not to mega evolve right away. The only reason anyone would run Mega-Absol is for Magic Bounce, which works best if you are switching in on a predicted status move, so you also want to Mega Evolve Absol right away.
Sir Mudkip is right - answering this would be a lot easier if you have a set example in mind.
If it really is a mega that should mega evolve right away, then it is possible that you were battling someone inexperienced at Pokemon. Just because a Pokemon's regular form is usually considered weak, don't immediately assume it is useless, though. To use the Mawile example from before, when was the last time you fought a regular Mawile? You haven't? Well, neither have I. Mawile is usually considered very weak without its mega, but even it can use Intimidate to weaken physical attackers, and so still has a use in its regular form.
If it didn't mega evolve at all, then how do you know the Pokemon was even a Mega, even if it was the only one capable of mega evolving on the opponent's team? It might not have even been holding its Mega Stone. Not every team runs a Mega. If it was a Mega that evolved later than you thought it should have, then the opponent may have even been trying to play mind games with you, by trying to fool you into thinking that it wasn't the mega, and so it was safe (for example) to switch in Breloom agaisnt Pinsir. All of a sudden Pinsir Mega-Evolves and OHKO's Breloom with an Aerialate Quick Attack. This is just an example I thought of off the top of my head, but there are better ways to play mind games by evolving (or not evolving) a mega.
I hope this answered your question, and if you have a specific example in mind then comment below and I will try to tell you why I think that happened with regard for the Pokemon in question.