The project you have attached is not complete. Please attach the complete project. You can do this from Project--> Archive workspace/project. Please do the following steps:
1. Unlock all the pins in PSoC Creator 'Pins' tab and try to build once. This gives the flexibility to PSoC Creator to use the best possible way to connect the pins.
2. Please check with code examples in PSoC Creator to check if there are any incorrect connections.
3. Please check the Analog tab in design wide resources to get an idea of how the internal analog routing is.
Please attach the complete project in case if already tried above mentioned points.
Here are a few things to consider:
I've run into a similar problem with the ADC_SAR_Seq component on the PSoC5. This component requires for some reason that each ADC input attached to the Amux needs to be directly connected to a Analog PSoC pin. Cypress never expressed why this was needed.
Evgeniy posted a modification of your project where each of the ADC inputs have a PSoC analog pin assigned. It compiles.
I've modified his project by:
I left the 'extra' analog pin assigned to the top of the Thermistor. It seems like a waste to have two physical PSoC pins assigned to the same node but without it, it doesn't compile.