Many a philosopher has 'identified' a problem of contradiction in Advaita System of Epistemology. One of them recently wrote in Prabuddha Bharata, a Vedanta journal of Ramakrishna Order published by Advaita Ashrama Calcutta, India:

The contradiction can be identified as, 'Mistaking a rope for snake involves misperception and the snake is supposed to last only for the duration of its knowledge. However, the Advaita theory of perception requires the existence of the object previous to the appearance of knowledge. This is of utmost importance because if the illusory object of perception does not exist prior to its perception it could easily be considered a projection (and not perception!).'

'This is thus clearly a contradiction between Advaitic theory of perception and the Advaitic theory of knowledge. Are we to put this contradiction down to the fact that the theory of perception adopted by Advaita Vedanta is rather crude on the scientific side, or is there a way to resolving the contradiction?' 

I am not a philosopher, but still I would venture to comment:

It is not puzzling to note that one sees contradictions (apparent or real) in the philosophic system of Advaita Vedanta; what really should puzzle a true Advaitin is the fact that someone is worried about such contradictions!

Only two categories of people would not see any contradiction in Advaita system:

(1) Those who have realized or experienced those principles for themselves, and 

(2) those who have nothing to do with Advaita.

To the lot of a few fortunate ones - third category, who are attracted by the wonders of Advaita principles but have not yet realized the truths thereof, would always come this state of mind of welcome confusion and contradictions. Doubts would linger till last.

Blessed are those who see contradiction in Advaita system of epistemology, for there is then a chance for these persons to attempt to go beyond the contradiction itself and become one with knowledge.

This is so because :

Transcendental Realization is expected culmination of study of Advaita Philosophy,

Transcendental Realization is expected goal of Advaitin,

Transcendental Realization is the only hope for Advaitin to come out of confusion.

The restlessness of the soul who theoretically wants to grasp all the nuances and subtleties of this system will find solace only in its logical growth of turning philosophy into religion; that Religion which is Realization!

Philosophic principles - ideas, thoughts, arguments, etc. - also act as quanta of particle physics. As seen through the prism of time, space, and causation the same Knowledge divides into two: seer and seen, knower and known, observer and observed, sense organ and sense object.

Discussion on Advaita philosophy presupposes the necessity of attempts at realization of this truth. Here philosophy and practice form one unit, attempt to discard any one would result in half hearted labor; futile.

But wonder of wonders is that the person who realizes the truth becomes 'out of world scientist': a mystic, a sage! He does no more relish the idea of discussing the philosophic intricacies. His experience makes him humble and silent.

Just as it is customary and appropriate for a scientist in physical science (or a philosopher) to have his laboratory, paper reading, seminars and conferences; similarly, this scientist of Vedanta science requires quietude and aloofness.

Renunciation, discrimination, simplicity, non-covetousness, and frugality are his natural mental attributes, just as debate and discussion are of a philosopher!

It is the growth of mind in a particular direction, brought about by particular way of sadhana, that makes a man capable of expressing spiritual Consciousness, to become Advaita Vedantin.