In the absence of performing forensic microbiology; an educated guess leads me to suggest that the core issue is sub-optimal cleaning and process sanitation. The outcome is spoilage due to any or all of the following opportunistic decay microbes Leuconostoc mesenteroides, Geotrichum candidum, and various yeasts. Warm temperatures, primarily, and reduced oxygen, to a lesser extent, will favor development of a slimy breakdown which can have a sweet to sour smell depending on which microbe is dominant and the extent/phase of spoilage. Shredding the carrots creates the opportunity for growth relatively rapidly although the microbes will also cause a sliminess in peeled carrot plugs with enough time and warmer than optimal storage temperatures.

With these microbes, routine post-cleaning and sanitation swabs will not pick up on a problem with Leuconostoc, generally the bacteria that starts the breakdown if optimal temperatures aren’t maintained. Media typically used for Aerobic Plate Count analysis may be blank but belts, blades, and other contact surfaces may harbor high populations of L.m. in hard to clean places. Swabs plated on media designed for lactic acid bacteria, such as MRS, will usually identify a site in the process that has become a reservoir for inoculation of carrots during processing.

Again, there may be a different causal relation that isn’t apparent from your description, but this is where I would start. --.