Is it permissible in Islamic law to take a commission from a merchant when purchasing fabric from him, knowing that this wastes time and causes dissatisfaction due to the practices of merchants?

It is not permissible to take a commission unless authorized by the employer. If the additional work conflicts with the original work, then either you inform the employer of your inability to combine the two jobs and ask them to regularize your situation if both are part of the contract, or you are not obligated to do the other work if only one of them is covered by the contract.