What you need to do first is look seriously at your board and schematic design for ground loops and improper ground couplings, as you seem to be aware of. You, because you post nothing for us to help you in that respect.
One thing you need to not do is randomly put inductances in there, as the other ninety of "it's 10/90 whether that accidentally even helps anything, by pure and utter coincidence" is it making everything unbelievably worse.
What most people do when powering high voltage and high current devices and sensitive logic tracks from the same power is called "star ground" and "star power", where all power tracks join only at one point, allowing their individual decoupling to catch the brunt of power spikes. Then follows the need for proper decoupling calculations, rather than "I put x and y on everything" you need "I calculated that the spike current here will be this, as such I need a capacitance of Y with an ESR of X (and possibly a maximum total inductance of Z) to have the power lines stay within the spec of the system as a whole" and then apply that with the type and number of caps that then implies.
Usually a first shot for high current motor peaks is calculate the capacitance and then make the ESR as low as your budget will let you across all, or most frequencies by decade-stepping: If you need 120uF, put a 100uF, a 10uF, a 10uF, a 1uF and a 100nF in parallel, where usually you'd opt for ceramic for all at or below 1uF. Then you cross off or combine those that you don't feel make sense. In this case I might make it 100uF, 22uF, 1uF. Then you find the best choices for those values that are inside the financial budget.
An easy way of forcing a star ground is using what 'the biz' calls "Net-Tie" elements. Basically a part that's just a high-lighted bit of wire in the schematic, but on the board is a two-pin element of a specific track size. One pin gets connected to your power-supply input and the other to the power-domain's ground and/or supply. For example you'd make a Net-Tie element of 8mil for your low-power logic and a Net-Tie element of 40mil for your power and put those next to each-other at the power plug. Or you put them opposite each other with the power plug in between.
This way Design Tule Checks will flag any "inappropriate intimacy" of your ground circuits.
One very important thing to be aware of, when using star-grounds, is that digital I/O controlling your motors needs careful planning and attention. If you drag them across a gap in your grounding system the return currents will need to go in a loop through your star-connection and possibly experience unwanted inductance, resistance or noise sensitivity. If you have a bunch of those, a separator element (opto-coupler or any one of a hundred many-channel capacitive-barrier chips) is often a good choice to keep out as much noise as possible. You can also opt to make the joint in domains such that you can route a single SPI bus across it, in desperate times, but it is noticeably inferior to proper ground and signal separation in the cases of coupled motor noise and such.
