Asking 59 people is obviously not a big sample size and therefore the results of this study are "not very reliable". To say it friendly.
And of course the researchers knew that. They weren't even trying to do what you imply. They weren't looking for reliably anything. Rather, they were looking for something interesting, along the lines of "are these interesting questions to pose in a much more expensive study that avoids the 2-5-year problem?"
Still, even with contemporaneous measurement, my guess is that there'd be a very real selection issue here; a non-random subset of people who could receive an autism diagnosis do, and to the extent the confounders into diagnosis (one presumes all the standard SES/race/access to healthcare factors are confounders here) constitutes a selection on the dependent variable, even a contemporaneous sample would not generalize to the population of interest.
It's not a critique of the study, either. You can't recruit tens of thousands of people for every little study.
So to rephrase, the headline could read "we found a relationship that probably doesn't actually hold, but just might".
The researchers conclude "Mothers of children with ASD have many significantly different metabolite levels compared to mothers of typically developing children at 2–5 years after birth."
And they back that conclusion up by describing their analytical process. If GP wants to dispute this conclusion, then the GP should explain why their method is flawed.