You have used ATCC cutures & checked the purity so no question of contamination . I can suggest that the cultures used for MR testing shoul be minimum 48 h grown as early stage culture may result false-positive MR.
Now a days even the ATCC also reported contaminant so check the purity of the culture by 16S rRNA . Following is one of case study for contamination in ATCC culture.
Article A Laboratory Case Study of Efficient Polyhydoxyalkonates Pro...
The methyl red test must not be performed unless the medium has been incubated for a minimum of 48 hours. Tests that are run too early may result in false-positive interpretation. It is important that a light inoculum be used. If an inoculum is too heavy, bacterial growth may be inhibited and result in invalid test results. False-positive VP results may occur if VP tests are read beyond one hour following the addition of reagents.