Negative values can occur in ACES files (and other floating point formats where they are allowed). Seeing negatives can be unnerving, but they are actually quite common to see in floating point image formats and IDTs from most camera manufacturers will result in some negative values even with "normal" images.
There are two main contributors that can cause cameras to produce negative ACES values from an IDT:
1) It is common for camera manufacturers to set the mean of their camera noise floor to map to zero. This means roughly half of all "black" noise will make pixel values with negative components.
2) Another cause is simple colorimetric error in the camera mapping of tristimulus inputs. Camera images are captured through color filter arrays that have spectral curves different from the color-matching functions. The mapping to colorimetry will thus have residual errors and can create one or more negative channels. In a camera's native RGB space, these may or may not be negative, depending on the encoding primaries used. In any RGB encoding space, negative values simply indicate that a pixel value projects outside of the triangle formed by the RGB primaries of the encoding gamut.
To help illustrate, below is a CIE 1931 x,y chromaticity diagram showing values sampled from a real image (the "SonyF35.StillLife.exr" image from the ACES developer 'images/aces' directory). You can see there are pixel values that project outside of the AP0 encoding primaries. I've labeled each area of the diagram to show whether the RGB's would be positive or negative for each section defined by extending a line along the sides of the encoding gamut triangle.
So, for example, the pixels projecting to the top right of the diagram - outside the AP0 triangle (and also the spectrum locus) - would have a negative blue channel.