An employer has the legal right to deduct overpayments from an employee’s pay without seeking the employee’s consent. So the main issue is whether you were overpaid for these times by clocking in earlier than you should have. This should be detailed in a workplace policy, for example the employer could have a specific requirement that you should only clock in when you start work, rather than when you arrive. It is not a legal requirement to clock in when you arrive. However, if there was no policy in place (you should check your contract for this and all workplace policies) then you can argue that the deductions were unlawful.
If this was the case then you would have normally had 3 months from the date of the deductions to make a claim for this in the employment tribunal, which you cannot do as you are out of time. You can however still try ad pursue it through the small claims court as a breach of contract claim as the time limit there is 6 years.
As to discrimination I am afraid that is unlikely to be a valid claim here as it only occurs if you are treated detrimentally due to your age, gender, race, religion, disability, etc – these are not the factors for your treatment here so it is unlikely to be discrimination which you can pursue.
Please take a quick second to leave a positive rating for the service so far by selecting 3, 4 or 5 stars above. I can continue answering follow up questions and in particular can also discuss the steps you need to follow if you are to make a claim for the deductions. There is no extra cost for this - leaving your rating now will not close the question and means we can still continue this discussion. Thank you