Why are some ATC call signs different than the flight number?
It's a solution to the Call-sign Confusion.


  Many large airlines operate call sign de-confliction programmes. These involve reviewing company call signs to ensure that aircraft with similar call signs are not likely to be routinely in the same airspace at the same time, and a process to systematically resolve ongoing issues arising from reports of similar call signs from their flight crew, ANSPs or other operators.


In busy airports, it's very common to have many flights with similar [sounding] call-signs (ATC perspective). You'd often hear the ATC stress the intended target.

Potential effects are:


  Loss of communication, loss of separation, level bust, AIRPROX, or midair collision.


However, passengers expect their bookings to be numbers, hence the split between ICAO call-sign (air traffic control) and IATA flight code (booking). From a marketing perspective, a changing IATA flight number isn't good for the customers and booking systems.

Taking TK656 (THY3YE) as an example, we also find TK65 and TK56. If one of those three were to return (emergency) or be delayed, it will add unnecessary confusion if it meets one of the others. There could very well be other operators with similar numbers in and out of Istanbul as well.


  Solution:
  
  Large operators should routinely consider using a combination of numeric and alphanumeric call sign formats.
  
  Guidelines:
  
  
  Avoid the use of similar call signs within the company
  Where practicable, proactively co-ordinate with other operators to minimize similar numeric and alphanumeric elements of call signs
  Avoid call signs with a four-number sequence; all-numeric call signs should be limited to a maximum of three digits
  Do not use the same digit repeated more than once (e.g. RUSHAIR 555)
  If letter suffixes are to be used with a preceding number sequence, limit the full string to a maximum of four alphanumeric components and, to the extent possible, coordinate letter combinations with other airspace and airport users
  Do not use alphanumeric call signs which have their last two letters as the destination’s ICAO location indicator (e.g. RUSHAIR 25LL for a flight inbound to London Heathrow)
  Where the total number of flights operated is large, it is likely to be best to use a combination of wholly some numeric and some alphanumeric call signs rather than all numeric or all alphanumeric
  If similarly-numbered call signs are unavoidable within a company, allow a significant time (at least 3 hours at any shared-use vicinity) and/or geographical split between aircraft using them
  If it is considered that useful capacity in the allocation of call signs has been reached, then consider applying for and using a second company call sign designator
  Do not use similar/reversed digits/letters in alphanumeric call-signs (e.g. RUSHAIR 87MB and RUSHAIR 78BM)
  For short haul flights, avoid using number sequences for particular routes which begin the day with ..01 and then continue sequentially through the day.
  
  
  —skybrary.aero [edited for proofreading]


Note: unlike the US, in Europe and elsewhere pronouncing numbers in a call sign requires saying each number individually, e.g. four-three-one-one, and not forty-three-eleven.