I suppose by "over" you mean "before" or "above in the sediment". A normal sequence of processes is that denitrification occurs higher in the sediment column than methanogenesis. Denitrification zone is followed (in the downward direction) by zones of Mn and Fe reduction, then sulfate reduction, and then methanogenesis. Some overlap is normal, but I would be very surprised if you indeed have methanogens outcompeting nitrate reducers. What is the system you are studying and what is the evidence for methanogenesis and denitrification? 

Mangrove litter may add carbon to the soil and cause methanogenesis over denitrification...

Methanogenesis occurs at the extreme redox conditions, and a fermentation process. Denitrification is a respiration process which requires an electron acceptor such as NO3. Facultative bacteria switch from respiration to fermentation process in the absence of O2 or in the absence of an electron acceptor (e.g. NO3, NO2, N2O, Fe3+, Mn4+). Both methanogenesis and denitrification require dissolved-C to fix C in the bacterial cells. I will be surprised if methanogenesis proceeds in the presence of NO3 in a microsite. Methanogenesis may be apparent in sediments with NO3 but the question is whether it occurred in microsites where NO3 or other electron acceptors were already depleted.