Flavonoids only constitutes a fraction of anti-oxidants. There are whole lots of antioxidant compounds present in plants. Low flavonoids content shouldn't be a benchmark. I recommend further analysis of total antioxidant capacity, free radical scavenging activity etc.
Its no only the flavonoids which are responsible for the antioxidant activities, there may be other compounds specially the phenolic compounds present. If you find out the total phenols then it will become clear.
Antioxidants are a combination of compounds and there are many parameters for it's assay. Make sure there is no other error in your experiment.
Some research say that Flavonoids is a type of polyphenol, but it is not necessary that flavonoid is the only antioxident in the plant, there are many more active ingredient in the plant. It's also depends on the part of plant understudy. In many cases it observed that flavonoids are predominant in plant root than leaves. Thus it is quit possible what you gets.
However I am sending you 2 publication might help you!!
Please tell me the protocol you are using for Antioxidant assay...
Article Evaluation of antioxidant, antibacterial, and antidiabetic p...
Article Evaluation of Phytochemicals, Antioxidant, Antibacterial and...
Antioxidant activity is a result of multiple components such as flavonoids, vitamins, and mineral elements in the extract. The observed low levels is not strange. Further analysis of other components that contributes to antioxidant needs to be analyzed in the extract.
All the peoples described the facts behind your results. However, you also could do a cross check. Collect another batch of sample, prepare new extract and perform the experiments again. These will make you clear about your findings.
Flavonoids content is not the signal of high activity, it depends on the compounds with potent antioxidant. Sometimes you may have high flavonoids content while the activity is low. many factors contribute to the antioxidant activity e.g the position and degree of hydroxyl group
First you try to minimise handling error of your experiment, cross-check the results and even then you see the same findings then it directly imply that antioxident contents does not depends only on the flavonoids, other secondary metabolites equally contribute to it which has been described by other colleagues.