There is a possibility of noise when you interface an external chip with FX which results in PHY/Link Errors on USB.
This issue will not occur if all our schematics and layout guidelines have been followed in your board. If this was the case, some ways to minimise the effect of PHY / Link Errors are:
Either re-work the board layout. Get it reviewed by Cypress Tech Support.
(i) Reduce the VIO power domain voltage levels
(ii) Use Clock instead of crystal
(iii) Change the voltage Swing using the SetTxSwing API (Enter Tx swing values by trial and error and find out which one has least effect of noise). Refer to API guide on how to use this API
- Madhu Sudhan