Is a trainee's secret taking of money from the bank where he is training a sin for which he must atone after three years?

If the bank deals with usury (riba), then it is forbidden to train there, and the wage received from it is unlawful (haram) and must be spent on the welfare of Muslims. What you did by taking the money in this manner is impermissible, and it is a betrayal of trust. Therefore, you must repent to Allah and return the money to the bank, even if indirectly. If you have wages due to you from the bank, request them directly. Assuming the bank is withholding your right and you cannot obtain it except through a stratagem, then it is permissible for you to take it, provided your person and honor are secure.