I not very clear with the picture you said.
1st of all, you need to know whether yourself are cover with EA or not.
Your salary need to be below RM 1500 or above RM 1500 BUT is a manual worker.
If you not cover with the EA, then you need to refer to your offer letter (1st priority). If your offer letter don't have write deduction then refer to your company "employee handbook" (2nd priority). If still don't have, then you need refer to your HR department (last opinion mostly is bad news =.=).
If you are cover with EA, then the company don't have the right to deduct your salary due to lateness. Unless you are late for 1 hour above then the salary may deduct based on pro rate or you get a warning letter.
Extra info, in the EA, company no need to provide transport allowance to employee unless you are girl/women that require work at night then you are entitled to it. So from my opinion, since your company already give extra RM 50 so it is consider good.