Beleaguered drugmaker Mylan NV’s third-quarter results on Wednesday might look pretty good. Don’t be fooled though; a financial hit from the EpiPen drug-pricing controversy is coming.

Analysts polled by FactSet estimate Mylan had adjusted earnings of $1.46 a share in the September quarter, up 3% from the same period a year ago. Revenue is expected to have increased 16% to $2.7 billion. And analysts at RBC Capital Markets reckon prescriptions of the lifesaving EpiPen allergy treatment rose through at least a portion of the...