Some authors can use variants of their last names in two different publications. How does one write their last name when citing both inline?

Inline citations should match what appears in bibliographies, and bibliographies should match what appears in the publication record. You can augment what’s listed—for instance, you could provide the original Cyrillic rendering in the bibliography to indicate the authors are in fact the same person—but I would leave the citation uncorrected.

You can use the correct (Mashchenko, 2013; Maschenko, 2015) version and address the issue that it might be misleading by explicitly stating that Mashchenko and Maschenko are the same author and perhaps by explaining why the issue has arisen.

The APA style blog addresses this and has some suggested wording: "Smith-Hartman (publishing as Smith, 2010)" blog.apastyle.org/apastyle/2017/05/… That may be not quite the right wording for a transliteration issue, though.

You could write "Мащенко (published as Mashchenko 2013; Maschenko 2015) found that..." This might be the simplest way to quickly address the confusion, while allowing the citations to match the bibliography and published record. (Other answers have nicely explained the importance of this.)