The question is so wide it's hard to answer. Here are a few options that come to mind:
1. You are doing the tests wrong. Too much bacteria, wrong media, wrong time of growth,...
2. Your extraction is wrong - wrong extraction solvent, temperature, etc.
3. You misidentified the plant you extracted (if you did extract a plant), or you are seeing the effect of ecotypes - geographical region, growth conditions, season, sun/shade, et.
4. The paper you looked at got one of the above wrong
5. Something else ...
I you want help try to define your question and conditions
You will test numerous strains and start with testing the highest concentration of product tested and low concentration of strain in solution 0.5 Mac Farland is sufisant.
Do other reports address precisely the same compound?
Disagree with above suggestions - that you modify your assay. The answer to unexpected results should not be retest or fix the assay. You should have run appropriate controls - so believe your data.
My take on this is that, the experimental conditions matters a lot. So check your experimental conditions and if need be adjust them accordingly what we call optimization . Se only, it should be known that barks terial behave differently at both phenotypes and genotype level. At one time you will find the compound working at phenotypic level simply be cause the bacteria was expressing the respective antimicrobial resistance genes at the time based on its environmental conditions while at some time later the same compounds don't work be ause those gene are not turn on at Molecular level thus the phynotypic activity is zero. Third as many other have said, the concentrations of the compound matters especially if it is a MIC being done. The drug kinetics and dynamics is very important here.