Why do the apostles baptise in the name of jesus, and not in the trinity as in matthew 28.",
Hello and thanks for the question.
Scripture does not contradict itself and when it appears to, it is necessary for us to look at the whole of Scripture for clarity. The same holds true for your question because it appears that the Apostles were not following the instruction given regarding the Great Commission to preach in the name of the Father, and of the Son, and of the Holy Ghost. Let's take a closer look by looking at Matthew 28:18-20.
Matthew 28:18-20 KJV
 And Jesus came and spake unto them, saying, All power is given unto me
in heaven and in earth.  Go ye therefore, and teach all nations, baptizing them in the name of
the Father, and of the Son, and of the Holy Ghost:  Teaching them to observe all things whatsoever I have commanded you: and, lo, I am with you alway, even unto the end of the world. Amen.
Notice what Jesus says in verse 18: ALL POWER in heaven and in earth is given to Me. In other words, Jesus has all power and authority and He is establishing this fact with the Apostles BEFORE giving them the Great Commission.
In the next verse (19), the Apostles are instructed to go, teach, baptize and "baptizing them IN THE NAME OF the Father, and of the Son, and of the Holy Ghost."
According to the dictionary, the term "in the name of" means that something is being done in accordance with their or its will or authority
. in this case, the Apostles are being authorized in IN THE NAME OF. Example: an ambassador is a diplomatic official of the highest rank, sent by one sovereign or state to another as its resident representative. A United States ambassador goes to other countries and officiates in official business "in the name of" the United States government. So, in turn, the Apostles are being authorized as ambassadors of Jesus to go, preach and baptize in His name.
Please note that the word "Name" is singular. Also note that the verse does not give us THE NAME even though from study we know that the three nouns are referring to the trinity. However, the text standing alone only provides descriptors (Father, Son, Holy Ghost) but it does not provide us with proper nouns like God and Jesus.
So the question is asked: What is the "proper noun" or actual name of the Person that is to be addressed in "IN THE NAME OF the Father, and of the Son and of the Holy Ghost?" Again take note that the verse says THE NAME and not the NAMES (plural) so we are looking for one name.
The answer is found in Acts 2:38.....
Acts 2:38 KJV
 Then Peter said unto them, Repent, and be baptized every one of you in THE NAME OF JESUS CHRIST
for the remission of sins, and ye shall receive the gift of the Holy Ghost.
Peter identifies IN THE NAME OF as Jesus Christ. A cursory reading of the text would suggest three different names but the text is pointing to one name.
Question: So how could the name of Jesus be the answer? Because according to Scripture, Jesus is the FULNESS of the GODHEAD in bodily form:
Colossians 2:9 KJV
 For in him dwelleth all the fulness of the Godhead bodily.
Matthew 28:19 authorizes the Apostles to baptize IN THE NAME OF but Acts 2:38 defines THE NAME as Jesus Christ. This is why all the Scriptures speaking of baptism during and after Pentecost speaks of the Apostles baptizing IN THE NAME OF Jesus. There are numerous Scriptures to validate this claim and I will share a few. First, let's verify that the Three are One.
1 John 5:7 KJV
 For there are three that bear record in heaven, the Father, the Word, and the Holy Ghost: and these three are one.
So baptizing in the name of Jesus is the same as baptizing in all three names since all three are one. Baptizing in the name of Jesus is not leaving out God or the Holy Spirit because the three are one.
The following text reveals God calling His Son God:
Hebrews 1:8-9 KJV
 But unto the Son he saith , Thy throne, O God, is for ever and ever
: a sceptre of righteousness is the sceptre of thy kingdom.  Thou hast loved righteousness, and hated iniquity; therefore God, even thy God, hath anointed thee with the oil of gladness above thy fellows.
As you might recall, Paul was arrested on the Damascus Road and was chosen by God to be the Apostle to the Gentiles. Paul perhaps boasted that he had been taught by God and not by man, yet Paul baptized in the name and authority of Jesus Christ like the other Apostles. God never corrected Paul nor the Apostles that they were not following His specific instructions.
Acts 19:4-5 KJV
 Then said Paul, John verily baptized with the baptism of repentance, saying unto the people, that they should believe on him which should come after him, that is, on Christ Jesus.  When they heard this , they were baptized in the name of the Lord Jesus.
I think the key to understanding what seems like a contradiction or acts of disobedience is to understand that "IN THE NAME OF" is signifying AUTHORITY. The apostles were to go, teach and baptize under the authority of Jesus and in the name of Jesus as was prefaced in Matthew 5:18.
The evidence from Scripture is numerous and conclusive that Jesus is the name of the Father, Son and Holy Ghost.
John 5:43 KJV
 I am come in my Father's name, and ye receive me not: if another shall come in his own name, him ye will receive.
And He also said the Holy Ghost would come in His name,
John 14:26 KJV
 But the Comforter, which is the Holy Ghost, whom the Father will send in my name, he shall teach you all things, and bring all things to your remembrance, whatsoever I have said unto you.
If Jesus came in the Father’s name, then the Father’s name must be Jesus, and if the Holy Ghost came in Jesus’ name, the name of the Holy Ghost must be Jesus. How can it be? Simply because Jesus is God the Father--the invisible Spirit manifest in the flesh,
1 Timothy 3:16 KJV
 And without controversy great is the mystery of godliness: God was manifest in the flesh
, justified in the Spirit, seen of angels, preached unto the Gentiles, believed on in the world, received up into glory.
John 1:1 KJV
 In the beginning was the Word, and the Word was with God, and the Word was God.
John 14:8-9 KJV
 Philip saith unto him, Lord, shew us the Father, and it sufficeth us.  Jesus saith unto him, Have I been so long time with you, and yet hast thou not known me, Philip? he that hath seen me hath seen the Father;
and how sayest thou then , Shew us the Father?
Another time Jesus said “I and my Father are one,” John 10:30. If Jesus and the Father are one, THE NAME IS ONE.
I do hope this response has been helpful. May God bless you as you study His Word.