You have to take derivatives with respect to x[t],y[t], not x,y, because that is the way f,g are written:
r = 1; b = 1; c = 1/100; \[Mu] = 4/10;
f = r*x[t] - b*x[t]^2 - c*x[t]*y[t] - 3/4*x[t]*y[t]/(a + x[t]);
g = -\[Mu]*y[t] + 3/4*x[t]*y[t]/(a + x[t]);
deq1 = x'[t] == f
deq2 = y'[t] == g
equilibrio = Solve[{f == 0, g == 0}, {x[t], y[t]}]
MatrixForm[jacobian = D[{f, g}, {{x[t], y[t]}}] // Simplify]
Simplify[MatrixForm[jacobian] /. equilibrio]
