This sentence uses "gedacht seien" instead of "gedacht sind" because this is indirect speech (triggered beiby "kritisieren, dass"). I would then expect "müssten" in the end, though.
The "Fülle" in Stofffülle means "large amount" here, so Stofffülle means "large amount of required material".
To translate the overall sentence, we can first look at its basic structure:
Schüler kritisieren, dass die Stunden verwendet werden müssen.
Students criticise that the classes have to be used.
Adding all the details leads us to:
Schüler kritisieren auch, dass die Intensivierungsstunden, die zum Üben gedacht seien, auf Grund der Stofffülle für neuen Stoff verwendet werden müssen.
Students also criticise that intensification classes, which are intended for practice, have to be used for new material due to the large amount of required material.