With a non-binding estimate, not every deviation is a problem. You generally have to accept a slight overrun, because an appraisal is not a precise promise. What is decisive is the threshold to a substantial overrun. The law sets no fixed percentage for this; whether an overrun is substantial is assessed case by case and according to the ratio of the extra costs to the original appraisal.
If an unavoidable substantial overrun emerges, the contractor is under a duty to notify. It must inform you without delay as soon as the overrun becomes apparent. If it omits this notice, it loses under section 1170a(2) ABGB any claim to the un-notified extra work. A cost increase presented only with the final invoice is therefore open to challenge, because the timely warning is missing.
If, by contrast, the contractor notifies the substantial overrun in good time, you have a choice. You can let the work continue, or you can withdraw from the contract against appropriate remuneration for the work already performed. In this way you are not forced to continue a project whose costs move clearly away from the original appraisal.