Their clear requirement is as following:
Employment requirements
- Completion of secondary school is required.
- A university degree or college diploma in business or public administration may be required.
- Experience in a senior clerical or executive secretarial position related to office administration is usually required.
- Project management certification may be required by some employers.
Now, have you gotten ECA done for both - BCA and MBA?
If Yes, does ECA says that your MBA is in Business Administration?
Also, have you matched your job responsibilities as per the selected NOC.
In short, if you can meet all requirements, I don't think you have a problem. However, if they only find your BCA eligible, there is a problem for sure.