The phrasing is correct and pretty normal, it’s just potentially ambiguous. English is like that sometimes. I’m not a grammarian, but I think “I counted all the yurts in Mongolia using machine learning” would normally be interpreted correctly by most people, with ‘using’ referring to the subject ‘I’. The way you’d write the other interpretation is “I counted all the yurts in Mongolia that use machine learning”. Your proposed alternative is also correct and less ambiguous.