What does 麻烦你了 mean? I understand the meaning of 麻烦 as "troublesome" (ex. 麻烦你等一下), but am not sure what it means in this phrase. 

I've heard that this can function as some sort of apology for troubling someone. Is that true?
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)