The depo injection is licensed for (I think, please someone correct me if wrong) 3 months, but it is actually effective for a couple of weeks longer than that. If you are going back on depo and your last one has already run out by the licensed dates (they work out the dates on a calender pretty thoroughly before you have the injection) you will be given a pregnancy test before they do the next injection, even if the injection is still technically effective. I had the depo continuously for about 2 years. A couple of times I was late in having the injection and each time I was late I had to have a pregnancy test before they came anywhere near me with the needle.
Having said that, yes pregnancy tests are not always 100% accurate, even the ones they do in the clinic. In the very very unlikely scenario that she was given another pregnancy test, which was also falsely negative, and she had the injection, it could potentially harm the foetus. But you have to remember there is a very low probability of two pregnancy tests being wrong.