Update: After reordering the metro consist I saw a train of the freight group (A pacific surfliner style consist) that was at the wrong height above the track and with all cars glitched into one. There indeed seems to be a max length after which consists get bugged.
Note: I also have the extra trains pack installed
@Walter @Benefactor69 @Alfa1561 I found the issue, I suspect the trains.xml is too long, as I am not sure what the cutoff is I just moved the metro configuration and the metro group configuration to the top (e.g. Metro Group right above Freight Group and Metro Config right above the Freight Confgis), this fixed the issue.