The product also has potential disadvantages: the very fact that the aligners are removable means they are not continually correcting the teeth. Unlike traditional fixed braces, they are largely dependent on a patient's habits and their consistency in wearing the aligners. The success of the Invisalign aligners is based on a patient's commitment to wear the aligners for a minimum of 20–22 hours per day, only removing them when they are eating, drinking, or brushing their teeth.

The system is also somewhat expensive, as conceded by the Align company, and can be more expensive than traditional wire and bracket systems.
The aligners must be removed before eating, an advantage and disadvantage depending upon the person. They and the teeth should be cleaned before re-inserting them afterwards.

Because the aligners are removed for eating, they could be lost. Invisalign recommends that the patient keep the previous aligners in case this happens. However, Invisalign provide two plastic containers to keep the braces in, so they are safe and can't be lost or damaged.

Certain teeth are slightly problematic for Invisalign aligners to rotate. Some lower premolars with their rounded shape can be difficult for the aligners to grasp and apply a rotational force to.

Unlike traditional braces, if a patient grinds or clenches her or his teeth during the day or while sleeping, the aligners can become damaged. In practice, however, this problem is very rare and a new aligner can be ordered. Also, similar to traditional metal braces, aligners may cause a slight lisp at the beginning of treatment. This usually disappears as the patient becomes used to the treatment.

The aligners are constructed of implantable-grade polyurethane, and the Align company has acknowledged that, though extremely rare, there may be cases of allergic and toxic sensitivity reactions to Invisalign. Minor symptoms such as sore throat, cough, and nausea have been reported.
Should the treatment go off track, or patients fail to keep the aligners in for the required length of time, then the next aligner in the series will not fit, and a new set of impressions and aligners will be necessary, adding to the cost.