My company never sent me on a pre employment medical im working there 3 years this has only come up because I have been to a routine medical within the company, will i get in trouble
As PP indicates, it was the company's error and not yours. So, unless you misled the company on your application form (e.g. by falsely answering 'No' to a question asking if you're colour blind) you're in the clear.
Has the realisation that you have not undergone a medical been the result of increased/recent absenteeism?
If this is the case, since you have been employed for more than two years they cannot fire you based on results of the medical (that they may otherwise have decided not to employ you).