Is HDPE affected by long term exposure to methanol?
HDPE should be fairly stable to MeOH, but it crazes in the presence of UV, when subject to oxidization or to environmental stress.

Since only some of the containers failed, were those subjected to more UV (e.g. placed by windows or at the front of a shelf in a well-lit location), placed near oxidizers, such as bleaches or were they subject to higher temperature, which would have caused the methanol liquid and vapor to expand, increasing pressure and stressing the container?

My experience has also been that apparently identical polyethylene containers have different failure rates, perhaps due to subtle differences during synthesis or manufacture.

Given polyethylene's tendency to craze, it might be best to use another type of container for long-term storage.

Note, though, that ~50% MeOH/water solution used for windshield antifreeze is usually shipped in polyethylene containers. Though the water lowers the vapor pressure, perhaps the UV susceptibility is addressed with additives.