This does happen on rare occasions. Inntel uses many distribution channels such as the GDS (Global Distribution System) and low cost aggregators, but suppliers do hold the right to offer the fare slightly cheaper on their own sites. If you do find an example, please let us know.
While it maybe slightly cheaper booking directly with the supplier, remember with Inntel you will be able to pay on account rather than having to pay by card and then expensing it. Your booking will also include traveller tracking in case of a disaster and will be included on your Management Information.