The bacteria took more time to double from 1 cell to a bottle full of cells. Once the bottle was full, each cell in the full bottle doubled, causing an additional bottle to be filled in 5 minutes. Then the 2 full bottles doubled in the next 5 minutes, causing all 3 bottles to be full.
Bacteria growth occurs exponentially; bacteria divides into 2 every t minutes (similar to the penny doubling every day story). If one gets filled, and the contents divides once, there will be enough for 2 bottles; when these two are ready to divide, there will be enough for 4. This growth process begins very slowly - 1, 2, 4, 8, 16, 32; but it soon speeds up greatly, 64, 128, 256, 512, 1024, 2048.