In the case of Israel and USSR , no, they knew perfectly what they were shooting at , and the decision to shoot down an airliner was given by the higher authority in full knowledge.. Look for the now published reports of Libyan B727 and the Korean707. In the case of Korean 007, we had to wait 10 years or so to get the Russian telephone transcripts that indicated that some Top brass thought it was a civilian airliner, while some others did not and ordered it shot down just in case. The transcripts are available on Wikipedia. In Iran now, yes it looks like they did not know what they were shooting at, like MH17and I excluded those. As to the USS Vincennes /IR case indeed I excluded from my list because we have a good report with exactly what failed and what happened from the US investigation board.
They are a lot more cases of voluntary shooting down civilian aircraft , in the cold war era , check El Al 402 by the Bulgarians in 1955 , or Malev 240 by the Lebanese. in 1975 , the 2 Rhodesians Viscounts airliners in 1978, DHL in Baghdad, etc... ..no misidentification , voluntary civil airliner shot down
And even this year last May , the east African Airways E120 Brasilia in Somalia ( shot down by Ethiopia) the list is long..