Yes,this puzzled me too initially,but if youre looking to build a PSoC based design,all you need is shown on the "Power System" diagram on Page 29.
Though do note,that its better to look at existing kit schematics,since this diagram isnt the whole picture.
Figure 2-4 shows the schematic for the PCB layout shown in figure 2-5.
According to the schematic, C13 and C14 are connected to P3 (pin 46) which is used as a bypass capacitor for the Delta Sigma ADC. There is an option in the ADC configuration Reference Section and "Internal Bypassed on P3.2".
The PCB layout snap is obscure in that portion. Thank you for bringing this to our notice.