Example matrices
A = rand(3); M = rand(3,1);
T = inv(s*eye(3)-A)
T =
From input 1 to output...
s^2 - 0.1414 s - 0.09975
1: ------------------------------------
s^3 - 0.6848 s^2 - 0.5428 s - 0.2312
0.2784 s + 0.3125
2: ------------------------------------
s^3 - 0.6848 s^2 - 0.5428 s - 0.2312
0.4245 s + 0.03184
3: ------------------------------------
s^3 - 0.6848 s^2 - 0.5428 s - 0.2312
From input 2 to output...
0.8448 s - 0.03394
1: ------------------------------------
s^3 - 0.6848 s^2 - 0.5428 s - 0.2312
s^2 - 0.6801 s - 0.2105
2: ------------------------------------
s^3 - 0.6848 s^2 - 0.5428 s - 0.2312
0.1216 s + 0.2926
3: ------------------------------------
s^3 - 0.6848 s^2 - 0.5428 s - 0.2312
From input 3 to output...
0.6707 s + 0.6945
1: ------------------------------------
s^3 - 0.6848 s^2 - 0.5428 s - 0.2312
0.8259 s - 0.2621
2: ------------------------------------
s^3 - 0.6848 s^2 - 0.5428 s - 0.2312
s^2 - 0.5481 s - 0.2326
3: ------------------------------------
s^3 - 0.6848 s^2 - 0.5428 s - 0.2312
Continuous-time transfer function.
H = T*M
H =
From input to output...
0.5751 s^8 + 0.02427 s^7 - 1.409 s^6 - 0.418 s^5 + 0.5442 s^4 + 0.6569 s^3 + 0.2698 s^2 + 0.05786 s + 0.003082
1: ----------------------------------------------------------------------------------------------------------------
s^9 - 2.054 s^8 - 0.2214 s^7 + 1.216 s^6 + 1.07 s^5 - 0.1777 s^4 - 0.5152 s^3 - 0.3141 s^2 - 0.08702 s - 0.01235
0.8913 s^8 - 1.494 s^7 - 0.2379 s^6 + 0.505 s^5 + 0.5066 s^4 + 0.03899 s^3 - 0.05927 s^2 - 0.03034 s - 0.003349
2: ----------------------------------------------------------------------------------------------------------------
s^9 - 2.054 s^8 - 0.2214 s^7 + 1.216 s^6 + 1.07 s^5 - 0.1777 s^4 - 0.5152 s^3 - 0.3141 s^2 - 0.08702 s - 0.01235
0.2092 s^8 - 0.04871 s^7 - 0.2243 s^6 - 0.4034 s^5 + 0.05266 s^4 + 0.2627 s^3 + 0.2117 s^2 + 0.07053 s + 0.01231
3: ----------------------------------------------------------------------------------------------------------------
s^9 - 2.054 s^8 - 0.2214 s^7 + 1.216 s^6 + 1.07 s^5 - 0.1777 s^4 - 0.5152 s^3 - 0.3141 s^2 - 0.08702 s - 0.01235
Continuous-time transfer function.
Your are correct that each element of H should have a third order denominator. But the Control Systems Toolbox doesn't "know" that every transfer function added together in H*M has the same denominator, so it does what it does and comes up with the general expression with a ninth order denominator (as would be obtained by adding fractions by first doing cross multiplication to form a common denominator).
You can get the expected result by applying minreal, albeit with a very high tolerance. minreal(H,1e-4)
ans =
From input to output...
0.5751 s^2 + 0.812 s + 0.05767
1: ------------------------------------
s^3 - 0.6848 s^2 - 0.5428 s - 0.2312
0.8913 s^2 - 0.2733 s - 0.06267
2: ------------------------------------
s^3 - 0.6848 s^2 - 0.5428 s - 0.2312
0.2092 s^2 + 0.2378 s + 0.2304
3: ------------------------------------
s^3 - 0.6848 s^2 - 0.5428 s - 0.2312
Continuous-time transfer function.
However, the correct approach is to not use inv and transfer function math in the first place. Rather, just build a ss model from the outset and go from there Now you can find poles, zeros, bodeplots, etc, w/o converting to a transfer function at all. There is no reason to do so. If you just want to see what the tf is, then tf(H)
ans =
From input to output...
0.5751 s^2 + 0.812 s + 0.05767
1: ------------------------------------
s^3 - 0.6848 s^2 - 0.5428 s - 0.2312
0.8913 s^2 - 0.2733 s - 0.06267
2: ------------------------------------
s^3 - 0.6848 s^2 - 0.5428 s - 0.2312
0.2092 s^2 + 0.2378 s + 0.2304
3: ------------------------------------
s^3 - 0.6848 s^2 - 0.5428 s - 0.2312
Continuous-time transfer function.
but all numeric computations should be done on the ss form of H.
I assumed that the "problem" is with usage of the Control System Toolbox. However, the tags on the question suggest that the Symbolic Math Toolbox might be in use. But, at least for this example, the SMT does not return the reported result
The common denominator in all terms is third order, as expected. The result can be simplified
vpa(simplify(H),5)
ans =

To get leading coefficient of the denomintaor to unity (to within a sign)
c = coeffs(den(ii),'all');
vpa(H,5)
ans =
