Strange. According to this RT article the reason was a sloppy assembly worker. Might be a coverup story of course.
"Later on, Russian media revealed the drill hole was made on the ground by a reckless assembly worker – he was identified and properly sanctioned, we were told.
Yet, the story does not end there. “There are drilling traces not only inside the living module [of the ISS], but also on anti-meteorite plates,” a space industry source told TASS news agency. These plates are mounted outside of the station’s hermetic hull.
“The one who made the hole in the hull passed straight through it and the drill head hit external non-hermetic protection,” the source explained.
Judging by previous media reports, there is a high probability of negligence. The worker in question apparently accidentally drilled the hole, but instead of reporting it, simply sealed it, according to Russian media.
The makeshift sealant held for at least the two months the Soyuz spacecraft spent in orbit, before finally drying up and being pushed out of the hole by air pressure. The ISS crew had noticed the drop of pressure in late August."
Could've been an intentional sabotage attempt? ISS crashing and burning would've robbed headlines for a good while.
https://www.rt.com/news/438443-iss-soyuz-drill-scratch/