In Harrington's second book, he talks about how people with very small M-ratios have to literally push any chance they get - especially in an unraised pot.
I think in your specific instance, you made correct choices, but just came out on the wrong end of it. It's not necessarily your responsibility, but you should be making decisions based on your pot odds and the range of hands your opponent may have.
Given their short stacks, that range of hands is quite large and usually calling with any two is also the proper move.
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