There are plausible answers to all of those questions, but the documentary just doesn't share them with you.
The dogs: the scent dogs actually tracked Halbach's scent to Steven Avery's own garage, showing much interest, and then continued to his trailer. A scent dog also alerted inside Avery's trailer. Zellner is just focussing on tracks away from the trailer and avoids mentioning all the tracks that incriminate Avery.
for example the scent alert at Kuss rd. What she doesn't tell the viewer is that this trail began at Steven Avery's own trailer.
she also doesn't mention the fact there is a scent trail from Steven Avery's trailer going all the way to where the RAV4 was found
the amount of DNA on the hood latch: just look at how the test is executed. She has some well rested tidy clean guys touch the hood latch. Steven wasn't well rested, nor clean. He was unkempt and in a rush to get rid of evidence, probably perspirating. The difference between 0,09ng and 1,8ng isn't a lot according to Meakin and Jamieson, two renowned DNA scientists.