What does 麻烦你了 mean?
The term 麻烦 can be a noun, an adjective or a verb

麻烦: (n) trouble; (adj) troublesome; (v)  to trouble / to bother / to inconvenience


  http://www.dictionary.com/browse/inconvenience
  
  *inconvenience
  
  
  verb (used with object), inconvenienced, inconveniencing.
  


As a verb, it has to be used with object

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 *I understand the meaning of 麻烦 as "troublesome" (ex. 麻烦你等一下)*


No,  "麻烦你等一下" means "(I have to) inconvenience you to wait a minute"


A better English phrasing would be "sorry to inconvenience you, please wait a moment " 


When you say 麻烦你, (inconvenience you), usually you would begin with a "sorry" . 

Since 麻烦你 itself already contains an apologizing tone, the "sorry" can be omitted.

*What does 麻烦你了 means*


It means:



"Sorry to inconvenience you" (to ask someone to do something) 


"Sorry to have inconvenienced you (to apologize for the inconvenience you caused)