“they.” This refers to all the disciples together. This is almost certainly the event recorded in 1 Corinthians 15:6 when he was seen by more than 500 believers at one time. There were not 500 disciples in Jerusalem, which is clear from the fact that there were only about 120 there around the Day of Pentecost (Acts 1:15). However, Jesus’ headquarters through most of his ministry had been Galilee, and thus the account of the more than 500 people who saw him at one time would have occurred there. The fact that he got with so many disciples at least partially explains why he would go to Galilee at all. There were many like Thomas who needed to see proof to be sure, and Jesus’ appearing in person in Galilee was surely a boost to the believers.
Although all the disciples “worshiped” Jesus, which in that culture meant to bow down before him or prostrate oneself before him, some of them “doubted.” This is understandable. Jesus told the Apostles over and over he was going to be killed and then raised from the dead, and it was such a foreign concept to them they did not understand the plain words he was speaking. The death and resurrection of the Messiah was a new concept to these Jews, and so it was natural that, even when they were faced with the living Christ, some of them “doubted;” they were not 100% sure of what they were seeing.
“bowed down before him.” See commentary on Matthew 2:2. Most versions translated proskuneō as “worship” here, but that is an unclear translation. The act of “worship” in that biblical culture was to fall down before someone, which is what these disciples did. That does not mean that they did not doubt at the same time. They bowed (or fell down) before him, but even in doing that act of showing respect, some were doubting.