Assuming that that paper is not false, it highlights lots of areas/reasons why things can go wrong.
Nonetheless, flawed as it is, the 'scientific method' is the best we've got. "How do you get people to discover reliable knowledge without getting sidetracked by bias, bribes, career incentives, corporations or politics" is actually a very hard problem to solve. The cobbled together bunch of institutions, practices and traditions that we call 'the scientific method' needs to be understood for what it is - a patchy, error prone but just about servicable method for fighting our own biases and shortcomings.
Always good to look for ways to improve it I guess but overly cynical or overly optimistic takes on it don't help much. We need to have a realistic view of it.