See image at https://commons.wikimedia.org/wiki/File:Citoid_results_in_VisualEditor_Screen_Shot_2015-04-02.png ISBN, DOI, and similar internal links are red. This doesn't appear when the citation is filled out via the "Cite web" option.
Can you tell me what input you put into citoid to get this? I think I know what may be happening, but for some reason I'm having trouble reproducing on my local install. This is in enwiki I assume?
Checked the fix in beta.
Note for testing: when checking in production - PMID, PMC, ISBN, and DOI are currently inserted as red, but turned blue after saving.
PMID, PMC, ISBN, and DOI should be inserted as blue initially.