When trials disagree...it can get ugly! But going into meta-analysis could help sort things out.
For a meta-analysis - a technique for combining the results of multiple trials - trials have to pretty much belong together. Differences might be responsible for contradictory results - including differences in the people in the trials, the way they were treated, or the way the trials were done. That's called heterogeneity. Too much of it, and the trials shouldn't be together. But heterogeneity isn't always a deal breaker.
Want to read more about heterogeneity in systematic reviews? Here's an article by Paul Glasziou and Sharon Sanders from Statistics in Medicine [PDF]. Or try the open learning materials from the Cochrane Collaboration.