追記です。
クリックによる選択からCtrl+Dまでの時間が短いとこの現象が起こるようです。
0.3秒で十分再現できます。

P.S.
This phenomenon seems to occur when the time between selection by clicking and Ctrl+D is short.
About 0.3 seconds is enough to reproduce this.

Oh yes. Now I understand that, and I must say I suffer from this myself all the time and had to ditched using Ctrl+D with width/height operations altogether, using it only for Move.

Glad that some one reported it, because I never had a time to start the investigation on this even.

Here are the steps for those who wants to get it:
1. Create a rectangle with a definite dimensions, like 30×10
2. Hold Alt and drag a copy of it below
3. Press Ctrl+D multiple times to get a column of similar rectangles — everything is OK so far
4. Now select the very first one, set the transformation reference point to the left, and change the width to a definite value, like 20
5. Select the one rectangle below and press Ctrl+D

You expect illustrator to repeat the transformation, and to get the same 20×10 rectangle you just made before. Instead, Illustrator changes the width to seemingly random values, like 15, 10, 5, minus infinity... Try to repeat pressing Ctrl+D for each of the rectangles below — each values will be different. The order can look like a progression or be completely random if you you try different shapes and dimensions.

As stated in one of the comments, pressing Undo and Ctrl+D after applies a correct transformation.

If you try older version of Illustrator, you’ll also get a position change, like if the transformation is applied from the original point of the originally transformed shape — and I believe this is what causes the bug.
It was fixed at some moment, but not fully. At least we don’t have the result we intend to get.

Thank you all so much for raising this up. I hope we can make something about it.

わかりにくいかもしれませんので、さらに補足します。
添付画像を用意しました。
Ten_Aさんの補足にあるように、1つを変形したら次の長方形 "だけ" を選択しなおすこととなります。
ただ、おかしさを実感するためには、なるべく素早く作業することが重要となります。

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Egor,
What he did was to click, Crtl+D, click, Ctrl+D, and repeat. Does this explain it?

わかりにくいかもしれませんので、私から補足します。
kamさんの見本の様に同一形状のものが並んでいてこれを個別に変形する場合において

1. 一番上の四角形を選択し変形パネルの幅を数値入力し変形させる。
2. 先の四角形の選択を解除し、直下にある四角形を選択する。
3. ⌘+D（変形の繰り返し）で変形する。
4. 選択を外し、以下同様に各四角形を「変形の繰り返し」で変形させる。
5. 変形させた各四角形の寸法が一定にならずばらつきが生じる。

変形の繰り返しで同一サイズの四角形を変形しているにも関わらずばらつきが生じるのはおかしいという指摘です。

Egor, Please refer below.
https://community.adobe.com/t5/illustratorフォーラム-discussions/変形の繰り返しバグ/td-p/12612737

わかりやすく

動画あげれない。

サブウインドウが録画されませんが、Wを変形した繰り返しCtrl+Dの連続でサイズがおかしくなる

Can you give exact steps to reproduce it?
Looking at the picture I don’t really understand what you tried to do.
A video will suffice too.