The Millimetre Astronomy Legacy Team 90 GHz (MALT90) survey has detected high-mass star-forming clumps with anomalous N$_2$H$^+$/HCO$^+$(1-0) integrated intensity ratios that are either unusually high (N$_2$H$^+$ rich) or unusually low (N$_2$H$^+$ poor). With 3 mm observations from the Australia Telescope Compact Array (ATCA), we imaged two N$_2$H$^+$ rich clumps, G333.234-00.061 and G345.144-00.216, and two N$_2$H$^+$ poor clumps, G351.409+00.567 and G353.229+00.672. In these clumps, the N$_2$H$^+$ rich anomalies arise from extreme self-absorption of the HCO$^+$ line. G333.234-00.061 contains two of the most massive protostellar cores known with diameters of less than 0.1 pc, separated by a projected distance of only 0.12 pc. Unexpectedly, the higher mass core appears to be at an earlier evolutionary stage than the lower mass core, which may suggest that two different epochs of high-mass star formation can occur in close proximity. Through careful analysis of the ATCA observations and MALT90 clumps (including the G333, NGC 6334, and NGC 6357 star formation regions), we find that N$_2$H$^+$ poor anomalies arise at clump-scales and are caused by lower relative abundances of N$_2$H$^+$ due to the distinct chemistry of H II regions or photodissociation regions.