The mistakes opened the way for archrival Ferrari, which rebounded from its worst start to an F1 season in 16 years to get reigning world champion Kimi Raikkonen back atop the podium.
"I was the first to say in Australia there won't be much in it," McLaren team principal Ron Dennis said after the race. "I would say the same now, and I will say the same in Bahrain."
Lewis Hamilton still leads the drivers' championship after two rounds with a win in Australia and a fifth-place showing in Malaysia, although team chief executive Martin Whitmarsh described his weekend performance as disappointing. Teammate Heikki Kovalainen finished third.
"There is no doubt Heikki progressed as the event went on," Whitmarsh said. "Heikki got to a more comfortable position with the balance of his car and it went away from Lewis.
"By Lewis' high standards, he would be disappointed with that."
Malaysia might have been the most challenging weekend of Hamilton's blossoming career.
Starting from ninth after his grid penalty, Hamilton began strongly on the softer tires, moving to fifth by the end of the first lap. But he soon became stuck behind the slower Red Bull of Mark Webber.
Hamilton looked close to ragged in his pursuit of the Australian driver, frequently locking his brakes and over-driving to the point that his tires had flat spots and delamination.
Still, he looked set to pass Webber in the first set of pit stops, until a pesky wheel-nut meant the mechanics had trouble removing the right front wheel. The stop took 20 seconds, so he emerged behind the Red Bull again.
The delay drew groans from his fans, but perhaps the more critical error was fitting another set of soft tires instead of the harder compound.
Hamilton struggled on the softer set, and when he was eventually fitted with the harder rubber in the second stop - and released in front of Webber- his speed increased and he almost caught fourth-place Jarno Trulli of Toyota.
"We are led by a combination of data and driver preference," Whitmarsh said of tire choice. "On the surface of it, it looks like we made a mistake, and we may have done.
"We made a decision; it may have been the wrong decision. We will analyze it."
Hamilton's problems in the race were made worse by the failure of the electronic drink system, leaving him parched in the hot and humid conditions.
"The great thing is that even though I didn't have any water, I was able to drive the race and I feel fine, better than last year," Hamilton told a race broadcaster. "We just have to make it work next time and do a better job in qualifying."