The Hab was simply not designed to last as long as Watney needs it to. It is a temporary shelter intended to last for 31 sols, and Watney keeps it in use for nearly fifteen times as long. With the strain he puts on the life support systems and his frequent use of the airlocks, it seems inevitable that some failure might occur during his time there. However, there were simple steps he could have taken to minimize the risk of catastrophic failure, such as the breach of the Hab canvas on sol 119.
The canvas sheet that ruptures, causing the breach, is AL102, the sheet connected to Airlock 1. During the initial storm that causes the abortion of the Mars mission, AL102 is hit particularly hard by the gale force winds.
Withstanding forces far greater than it was designed for, it rippled violently against the airlock seal-strip. Other sections of canvas undulated along their seal-strips together, acting as a single sheet, but AL201 had no such luxury. The airlock barely moved, leaving AL102 to take the full force of the tempest.
This results in a weak spot along the seam of the canvas. Although Watney inspects the Hab after the storm, he doesn't notice the weakness, as it is concealed by a seal-strip. It is possible that had Watney performed a more thorough check of the canvas, he would have detected this weakness early and avoided using Airlock 1 to prevent further strain on the seam.
However, quite the opposite, Watney uses Airlock 1 more than either of the other airlocks because of its proximity to the rovers. While this is understandable to reduce EVA time, by favoring Airlock 1 he fails to distribute the pressure put on the airlocks evenly, resulting in increased stress on the canvas around Airlock 1 and specifically AL102. Each use of the airlock weakens the canvas further.
When pressurized, the airlock expanded slightly; when depressurized, it shrunk. Every time the astronaut used the airlock, the strain on AL102 relaxed, then tightened anew.
Pulling, stressing, weakening, stretching . . .
If Watney had completed a more thorough inspection of the Hab after the initial storm, and if he had kept his use of the three airlocks balanced, he might not have been able to fully prevent a Hab failure. However, he certainly could have minimized the chance that certain portions of the Hab were put under the kind of consistent, imbalanced pressure that could result in the life-threatening breach that did occur.