The entire fight with Super #17, from the start with the Zet Senshi to the end with #18, was sloppy at best. Goten and Trunks lasted longer than Gohan, Vegeta may or may not have even transformed to Super Saiyan 2 until the end, and Goku only went Super Saiyan against someone he watched tool everyone else. All of it could be due to Toei not giving a shit about consistency and only about entertainment value.
Goku only seems to use Super Saiyan and then Super Saiyan 4 once he gains it, never really Super Saiyan 3 and even rarer is Super Saiyan 2, which is a shame. Hell, I don't think Goku went Super Saiyan once after the Super #17 battle. Toei gradually phased out every other form for him.
Anyway, to get to the main point, because the fight is so odd and factoring in Toei's tendency to bolster Goku's strength to whatever they feel is cool regardless of logic, it's very possible he was stronger than Super Saiyan 2 Vegeta. At the same time, it's possible because the machine mutant was toying with everyone that it's all up in the air.