For me, it's somewhat that you have to take some of these things with a grain of salt...
One source is interesting. Two [independent] sources starts to look meaningful... Three starts to become pretty compelling evidence of a proposition.
Science is somewhat of a random [drunken] walk in the general direction of the truth. Any reasonably interesting proposition has to be narrowly enough true or false and complex enough to merit study or it's something we all know as obvious. So you can imagine that sometimes small differences in things like study design can suss out opposite conclusions from each other between two groups doing research.
That's not a flaw. It's just part of the process.
