Firstly, you can't identify the Fake Form 16 against original.....
but I would suggest, that
Read out the clauses carefully compared to the original one and look out for the official seal if it's already been executed....
Secondly, collect the company related original details of deductions and ask for the verification slip from the company,
and in case of huge fraud or misrepresentation you may take the assistance from Income tax department giving the employee tax code details to them and lodge a complaint .....
For more details call toll free number 18001801962 , and ask them what are the steps they have taken to prevent the fraud and also how to make out fake against original........ (It's a Toll Free Government Official Number, Ayakar Seva Kendras)
(Infact, I did call them up, first tie call was disconnected, second time I spoke to a person who cold not at all grasp the question and said he would transfer the call to his senior later after waiting for few minutes he said the senior is busy and there is only one form 16! I thought there is no point in continuing the conversation so i said I would call them later.... funny and weird experiences!! but relying on official sources in many matters is just waste of time..... )
But, cross verifying with the company who have issued the acknowledgements is the best way to make out.......