Assuming you properly sanitized and flushed the outlet (removed screen from faucet etc.) and there wasn't a sampling error, my assumption would be that the lines were contaminated during installation. Perhaps test the water coming out of the wall connection before it passes through the sink, that would help you know if the contamination came from the water itself or from the sink.
IBWA has a coliform retesting procedure for bottled water that would be somewhat valid for you to use in your follow up testing:
If positive for total coliform, an E. coli determination is performed from that test. When a unit of production results in a positive result for coliform organisms by a total coliform method in Standard Methods for the Examination of Water and Wastewater, 20th Edition, the following policy and procedure should be employed:
1. Immediately analyze 10 additional samples from the same production lot for total coliform. Also examine the original sample for presence of Escherichia coli (E. coli) by a method in Standard Methods, 20th Edition.
2. Review sampling and analytical procedures to determine if the original sample contamination may have occurred due to sampling or laboratory error. If the review of sampling and analytical procedures demonstrates a source of contamination, such as contaminated media or analyst error, INVALIDATE results and proceed with total coliform analysis of five additional samples from the same lot using uncontaminated media and proper technique.
3. Company plant personnel should use the following guidelines for decisions on the disposition of the lot: a. If the re-sampling does not show E. coli or total coliform, consider the first sample an invalid result. b. If the original sample AND any of the additional four samples collected are positive for total coliforms or E. coli, consider the results valid and conduct follow up actions pursuant to the company’s plan.
If it is contamination at the sink, then you could somehow plumb the fittings up to some pressurized sanitizer and essentially CIP the internal components (chlorine would work well since presumably the sink's materials should be somewhat resistant). Alternatively it may be easier/cheaper to just replace the faucet and fittings on the sink. Then talk about handling them in a sanitary manner with your maintenance crew, who may have done the drain plumbing first then worked with the water connections without a hand wash in between.