The most likely cause is inconsistent processing rather than the camera changing exposure settings. Since the files are DNG/RAW, your software may be applying automatic color adjustments such as auto white balance, which can vary from frame to frame—especially in difficult twilight lighting. That kind of variation shows up as color flicker in a hyperlapse.

To prevent it, make sure no automatic color setting is being applied in post. Select all frames and synchronize a fixed manual white balance and any other color/tone settings across the whole sequence. For future shoots and edits, keep everything as manual and consistent as possible so each frame is processed identically.