Awkward Financial situation

TLDR; Don't know if I'm over reacting due to me being naive, I missed out on pay raise and wondering if I can somewhat fix the missing raise in some way or another.

Work in a small tech company for a few years, started as a salary based junior. The contract stated that that yearly reviews has a chance for a raise. I did not realize that this was something I had to request, for the meeting, rather than like my previous workplace where it was scheduled by the leads/HR themselves. The first year work was pretty busy so time flew by pretty fast before I knew it and I guess I was getting above average for my position already. During my 2nd year, I found out that we had to request for the review, A few of us were missing out so we all decided to message the person who was to organize it, there was a bit of back and forth with them being busy, so we continued to nudge them every now and then for the request, 4-5 months go by and a coworker said he was gonna have his meet soon, so I followed up with the person and was told "I'm on the list" few weeks go by and nothing happened, but sometime later I noticed my take home amount raised, yay.

After, a project finally finished and then was put on standby with another coworker, we were idle for a few months. An amount that felt a little bit worrisome with "things were in the works", but I guess we survived the layoffs. The "Shady" part is that there were other projects going in the background while we were idle, so I do not know if this was 退職勧奨 Voluntary Quitting play or just minor mismanagment. We managed get on other projects afterwards after multiple follow-ups

Another fact was when I finally starting to do some household accounting stuff when I noticed that my base pay as been the same, but an extra amount was allocated to an "Allowance" category.

I felt a bit uncomfortable with being on the sidelines for a prolonged period of time, making me feel like I was cheap enough "to hold on to" or the force-out, but I am unsure if this is a common thing in or not in this industry over here.

Is it possible to negotiate for the pay gap, or better of the alternative because the "allowance" feels somewhat shady to me. The downside is my Japanese is still not proficient enough to talk fluently, and might be hard to find another place.

Edit : some extra info

by Tachi25