I have a design with embedded board ( EFUS) with Linux , together with a CY8C24894-24LTXI.
On the cypress is connected a CTS keyboard ( touch detection of keys) .
When the board is running , i have on the inputs unwanted signals ( even if my keyboard is disconnected). ( see picture fig004)
Under the cypress, there is no plane and no high speed signal around
Also the power on the cypress is clean
It seems there is direct radiation into the cypress.
You will get some counts even if the CapSense button is not connected, since every GPIO has some capacitance. The counts you are getting is acceptable. All the counts are less than the threshold, which means that there are no false touches.