If you were physically present in California for this internship, even if it was only temporarily, you should be paying California income tax on the income from the internship. To do this, you would have to complete a California nonresident tax return and select the portion of your wages that were earned while in California to be taxed by California.
Once you complete the California nonresident tax return, you should receive a credit for the taxes paid to California on your Illinois return. If your employer was not withholding California taxes for the internship, that does not mean that you do not have to pay their income tax.
Once the California return is completed, the Schedule CR should fill out accurately and not prevent electronic filing for Illinois.
