For someone who sweeps a loop for a switcher for the first time can be tricky, especially regarding injection levels. Rinj values, conduction mode etc.
Below is my general procedure I have used to sweep many control loops successfully:
1/ Before you can sweep the loop, you must get the system stable, otherwise you will get garbage results.
Looking at your scope plots, it appears that there are signs of instability from the burst oscillations on a 100 Hz ripple. Since the 3525 doesn't have a burst mode, it is most probably instability. Slow the loop down as previously suggested and make sure you get it into a constant conduction mode.
2/ Since the loop gain will be at the highest near the low-frequency start of your sweep, you will need to inject at a higher amplitude. I normally use Rinj value between 33 and 50 ohm. The 5 ohm in the setup diagram seems too low in my experience and will make it difficult to drive at low frequency, where you need the extra amplitude.
3/ One of the pre checks I do (with the loop stable) is to just manually sweep the freq injection from my function gen, while looking at the PSU output (AC coupled, lowest BW, Avg) on one channel and the triggered input on another channel. What I am looking for is to see that I get a good response on the output (the same un-distorted sine shape) as the one I am injecting. Some switching noise on the sine is normal, as long as the sine shape looks good. This noise will be suppressed by your instrument measurement software using a narrow RBW during the actual bode sweep. I will up the injection signal to get higher SNR level if needed, as long as I don't see any distortion on the sine riding on the output voltage. You don't want to see the sine wave with clipped tops or start looking like a triangular wave. I will note the level that gives a good shape up until about 1 kHz.
4/ After 1 kHz, you can normally drop down to around 10- 20 mVrms, since the loop gain also drops off with frequency. So, you need to taper your level from high to low as the frequency increase in most cases.
5/ With these levels in mind, I set up my synchronized bode sweep with an RBW low enough (1 Hz to 10 Hz) to reject the switching noise. You can also use averaging sampling if you need more noise rejection, but it will increase sweeping times.
6/ Run the sweep and see how clean the phase plot comes out, as phase is the most sensitive of the measurements. The region you will be most interested in, will be around the point where the gain plot crosses the 0 dB line. Sometimes you may tweak the levels a bit to get the best response.
7/ You want your phase margin to be more than 45 deg, more like 55 to 60 to be safe. Higher margins will give a more damped but slower response with less overshoot. I am happy when my gain margin sits at about 10-12 dB.
8/ Once you get acceptable results you can start messing around with the compensation values (small tweaks at a time, re sweep) to increase the loop BW and speed up the transient response. Take your time, don't rush.
Here is a helpful vid by OMICRON lab that explain some techniques and results.
I also include an old document by CleverScope on FRA sweeps where they use a Jensen VB-1BB video isolation transformer for injection. These are often available used for below $50.