I have contacted ICANN Compliance, following the Group's discussion on Charter Question e)
The current registry agreements include a broad variety of obligations (most of which are very technical in nature), spread through the body of the agreements themselves and their many appendices (up to 11). For most of those obligations there are no graded sanctions or penalties, which means that if a registry is in violation of any obligation, receives the 1st, 2nd and 3rd notices, is then issued a notice of breach and still doesn't cure, it could go to termination without any penalties in between.
However, some of the agreements include an appendix specific to SLAs (service level agreements). These SLAs provide that when the registry operators fail to comply with their Technical and Performance Specifications, they have to apply credits to the registrars' fees, depending on the specification that was not met and the impact. The SLAs provide tables that explain what credits apply for each type of specification. See one as an example: http://www.icann.org/en/about/agreements/registries/info/appendix-10-08dec06-en.htm .
These credits, although not technically penalties, do affect the registries negatively.