There are four lists of the disciples found in Scripture. They sometimes differ in order, but this is not a problem since listing people in a different order still demonstrates that the people were the same. Matthew, Mark, and Luke, each contain a list of 12 disciples. However, Acts contains only 11. This is because Judas Iscariot, who had betrayed Christ, had died and was not listed. Acts 1:21-26 tells how they replaced Judas with Matthias thus retaining 12 disciples.
As you can see from the chart below, the disciples are listed according to each section of Scripture. The difference in content occurs with Thaddaeus and Judas the son of James. The most logical explanation is that both names describe the same person. Afterall, Judas the son of James would have been sharing the name of Judas Iscariot, the betrayer of Christ. It's highly probable that he preferred to be called Thaddeus.
It is common in Scripture to demonstrate people's alternate names. Take for example Acts 1:23 where we see that someone named Joseph is also called Barsabbas and Justus.
|Matthew 10:2-4||Mark 3:13-19||Luke 6:12-16||Acts 1:13-14|
|Simon (Peter)||Simon (Peter)||Simon (Peter)||Peter|
|James, son of Zebedee||James, son of Zebedee||James||James|
|John, the brother of James||John, the brother of James||John||John|
|James, son of Alphaeus||James, son of Alphaeus||James, son of Alphaeus||James, son of Alphaeus|
|Simon the Zealot||Simon the Zealot||Simon the Zealot||Simon the Zealot|
|Judas Iscariot||Judas Iscariot||Judas Iscariot||-----|
|-----||-----||Judas the son of James||Judas the son of James|
|(Matthias who was later chosen in Acts 1:21-26)|