A Czech native speaker told me that this phrase could also mean 'I am very clumsy' or 'I have messed up' as the name 'Matej' is referred to as a clumsy person. (equivalent to Kevin in German language).
What is the difference between "jsem Matej" and
"Já jsem Matěj."?
Essentially, there is no difference. Please see my comment above.
Huh i thought czech names are similiar to russian
There is similar Russian name: «Матвей».
Doesn't this translate as "I, I am Matej"? Doesn't jsem Matej mean "I am Matej"?
"I am Matěj" could be written without or without "já," and the meaning would be the same. In Czech it's very common for pronouns to be omitted when they represent the subject of the sentence.
I hear 3 M: Já jseM M Matej
Is the pronunciation correct?
Hi, no there are only 2 M: Já jseM Matěj. There is nothing between "jseM" and "Matěj".
I hear two Ms in the sentence. Typically in English you'd just say them together, like "them mice". Is is it the same in Czech?
You should indeed hear two M's, unlike in English.