How should one acknowledge a funding agency if it fulfils its obligations only partially?
Since you did get support from your funding body, you will need to list it in the funding acknowledgements. This doesn't change with the fact that you have also gotten support from elsewhere. As profmartinez wrote, the proper term is to state that they provided partial support. Some researchers write "partly" exclusively in their funding acknowledgements, as their home institutions provide some level of support as well (offices, ...), which are not normally acknowledged.

The fact that your funding source provided less support than expected should not be written into the funding acknowledgements. Mentioning this somewhere would in the best case have no effect. In the worst case, it makes a bad impression both on you and the funding body. You have no ethical obligation to mention the quirks of their funding scheme, and under the "choose your battles wisely" premise, not mentioning the problem is the way to go.