The Celtic Park side also face a further two charges for kit infringement and stairway blocking.
One of the banners, visible in the north east corner, where fans group the Green Brigade are usually situated, showed a paramilitary image.
Celtic will likely face a fine for the banners. They were handed a £8615 fine last year in the Champions League qualifiers after supporters displayed Palestine flags during the match against Israeli side Hapoel Beer-Sheva.
The charge of kit infringement relates to the logo of sponsors Magners being visible on substitute bibs. It is an offence under the rules of the governing body to advertise alcohol, though STV are reporting Celtic will likely get off with a warning.
The case, dealt with by Uefa’s Control, Ethics and Disciplinary Body, will be determined on 28 July.
A UEFA spokesperson said: “The ‘illicit banner’ charge relates to the banner portraying a person in a paramilitary uniform.”