Yes certainly it is possible. We were unaware of microorganisms till the microscope was invented.
If some organism whose temporal perception is much longer than ours, say a single thought or action of it takes centuries or millennia to form, we may be unable to perceive its actions.
Our brains may also be unable to process or even imagine certain phenomena and we wouldn't even know it. Like other animals are unable to think of calculus.
However, if some entity/thing have a material effect on our world, we may be able to deduce their existence. The existence of genes which are responsible to heritability was deduced long before DNA was discovered. — debd
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