Hello andrey.d
I can suggest to use higher tie point limit in the Align Photos dialog (like 4,000 - 8,000) and try using High accuracy. Also make sure that in the Camera Calibration window all distortion coefficients prior to the camera alignment are zeros.
During optimization you can use Rolling Shutter compensation flag to correct the related issues (many users report that have problems aligning RGB Sequoia camera images due to the rolling shutter effect).
In addition prior to the optimization I recommend to check if there are any misaligned cameras (could be "stacked" to the same position) and reset alignment for them.