Why does grid-gap cause an overflow?

If you want to use percentages or some other unit, there is one more solution. The use of the minmax() function will allow the columns to shrink to fit the parent container and not cause overflow.

The solution would look like this:

grid-template-columns: minmax(auto, 25%) minmax(auto, 50%) minmax(auto, 25%);
gap: 10px;

More on the minmax() function here.

Short Answer

Because the width of the columns plus the width of the gaps is greater than 100%.

Explanation

You have a 3-column grid container (.body):

grid-template-columns: 25% 50% 25%

The total width of those columns is 100%.

You're then adding gutters between the columns (and rows):

grid-gap: 10px

which is shorthand for:

grid-column-gap: 10px;
grid-row-gap: 10px;

So this becomes the width calculation:

25% + 50% + 25% + 10px + 10px

Hence,

100% + 20px > 100%, which results in an overflow condition

Note that the grid-*-gap properties apply only between grid items – never between items and the container. That's why we calculate two grid gaps, not four.

As a solution, instead of percentage units, try using fr units, which apply only to free space. This means that fr lengths are calculated after any grid-gap lengths are applied.

grid-template-columns: 1fr 2fr 1fr

div:not(.header):not(.body):not(.row) {
  border: 1px solid grey;
}

.header {
  margin-top: 20px;
  display: grid;
  grid-gap: 10px;
  grid-template-areas: "header-left header-right-up" "header-left header-right-down";
  grid-template-rows: 40px 40px;
  grid-template-columns: minmax(50px, 200px) auto;
}

.header-left {
  grid-area: header-left;
}

.header-right-up {
  grid-area: header-right-up;
}

.header-right-down {
  grid-area: header-right-down;
}

.body {
  margin-top: 20px;
  display: grid;
  grid-template-columns: 1fr 2fr 1fr; /* ADJUSTMENT */
  grid-auto-rows: 80px;
  grid-gap: 10px;
}

.row-left {}

.row-center {}

.row-right {}

<div class="header">
  <div class="header-left">image</div>
  <div class="header-right-up">content</div>
  <div class="header-right-down">long content</div>
</div>

<div class="body">
  <div class="row-left"></div>
  <div class="row-center"></div>
  <div class="row-right"></div>

  <div class="row-left"></div>
  <div class="row-center"></div>
  <div class="row-right"></div>

  <div class="row-left"></div>
  <div class="row-center"></div>
  <div class="row-right"></div>
</div>

revised codepen demo

More details here: The difference between percentage and fr units