English Translation
Mary told him not to waste her time.
Should this possibly be “le hiciera perder el tiempo”? 
It’s probably because it’s “her time” and not “his time”?
I was thinking that “el tiempo” is the direct object, so his/her would have to be expressed using the dative pronoun, like in Italian and French. But one should of course be wary of drawing conclusions from other languages, however closely related they may be.
The way I understand this sentence is literally “Mary told him not to make her lose time”
la hiciera perder - make her lose
le hiciera perder - make him lose
Google agrees insofar as if you change “la” to “le”, the translation changes to “waste his time”.
And if you put my literal english translation into google, you get the exact same spanish sentence out.
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I agree with your analysis, but only in the intransitive use of perder.
The only other similar sentence I’ve found is this:Es imposible hacerle entender la teoría a ella.
English Translation
Mary told him not to waste her time.
I’m still wondering about this.