Possible wrong use of TVS diodes?
The idea is correct. 

But check the followings:


the TVS for 26V is not a proper choice for the 24V input. Remove the TVS from the 24V input (you shall put there a tvs with a voltage over 30V as a protection). Same applies to all 24V inputs. 
consider how TVS works: it will go short once the breakdown voltage is exceeded. Ensure that there is a component where voltage can drop, otherwise it will cause a heavy ground bounce in your circuit. For example, an input pin can look like: pin - series 330 ohm resistor - TVS to gnd, which allows the resistor to dissipate the excessive power caused by an over-voltage
note that TVS very likely can not trip a fuse, definitely not a 3A fuse (that requires like 6A to trip). TVS are for protecting short ESD style pulses, if you want to trip a fuse, use a varistor as a slower (but more rugged) device.
I think that in your case, the TVS will be tripped because its maximum breakdown voltage is 26V, and it may trip at 24V. This causes a serious ground bounce, causing the port protecting diodes of the microcontroller to open, and the reverse current makes the micro heating up.


I found it is a good idea to have a multi-level of protection, and use the TVS for ESD protection (instead of very narrow overvoltage protection). The data sheet says its maximum breakdown voltage is 26V, so actually it can start conducting at 24V or at 23V as well.

So it is a good idea to:


use some other mechanism as a rough primary protection (e.g. varistor, spark gaps, PCB inductors - refer to security panels and PIR sensors of a good example on this)
have some series resistance, and use the TVS as a secondary protection. Note that the series resistance together with the capacitance of the TVS will cause a low pass filter, so in some high-speed applications (e.g. USB) you can not afford having a series resistor.


the TVS shall be a little higher voltage than the allowed max. TVS have max trip and min trip voltages - the min-trip must be above the allowed max normal input.
note that even though you do have a TVS, there is a chance of an overvoltage because the TVS tripping point is not really precise. Therefore use another series resistor of say, 100-470 ohm, before connecting to the microcontroller.
the port diodes inside the microcontroller will clip the voltage in a reasonable range. Thanks to the series resistor, even though these diodes can survive less than 20mA, everything is protected and still in the safe area.