When the dog 'Buddy' drank, or put his muzzle into the water, he died almost instantly. We would have expected dozens of dead animals (deer, etc.) in the forest in that area if the toxic waste had been dumped there multiple times, which seems to be the premise.
The toxic waste changes color between orange and pink. Possibly due to inconsistent color correction.
After 'buddy' the dog dies Macgyver comes up to him and 'buddy' blinks his eyes.
In the beginning, Toberman gets shot with a shotgun, but his leg wound is very localized. A shotgun sprays pellets, so the expected wound would be much more widespread.