I would like to ask some question regarding concrete cover for
foundation base for a 3-storey office building.

The pipe cap (1100 L x 600 W x600 H) under group 2 piles have U-shaped Y16 on both direction X and Y. Top surface of pipe cap is cut / empty.

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Reinforcement concrete note:
- 50mm conc. Cover shall be provided to all structural concrete base at ground level;
- Concrete cover to main bar (Not otherwise shown)
a) Foundation base - 50mm

Question:
Bottom concrete cover is 50mm. How about both sides(vertical bar)?
Is it still 50mm? My manager said it is 25mm...

This question appears to require an interpretation of drawings and/or specifications. The designer/engineer/architect should provide the answer, if there is not agreement on the project. You evidently do not agree with your manager's interpretation. I think that you have 3 choices. Convince your boss that you are right and he/she is wrong, accept your manager's interpretation, or get an OK to discuss the matter with the designer.