Auto Lap not very accurate

Not clear by "stadium" - if indoors or limited view of the sky GPS will not be accurate enough to come close to hitting 400m right on.  Even in good conditions, it will still be off.  You could try a foot pod - if well calibrated (or something like the stryd), and set the activity for indoors with distance from the foot pod this may be more accurate..  As far as I know pushing the lap button just adds a new lap so the next auto-lap starts from there (happy to be told that this is incorrect).  There are some good datafields (Peter's Race Pacer) that will adjust the pace and likely race time based on hitting the lap buttons close to the selected markers  but more designed for longer races.

Ultimately, I would suspect your best bet is to turn autolap off and manually hit the lap button (as it sounds like you planned on doing this anyway).

Edit:  Should have added that it is pretty hard to actually run  a perfect 400 m on a lap unless you run accurately in lane 1 (and assuming the track is properly measured) - although I suspect you know this.

Depending on which lane you are running on the stadium track, it sounds correct. There is nothing wrong with the auto lap and there is nothing wrong about your fenix 5.

Only the inner most lane marking on the track is exactly 400m, even if you are running on lane 1 unless you are running on the left marking of lane 1, you are running more than 400m each round, it is simple mathematics, as the radius is not the same. So every round will add a little more to the 400m.

See extract from https://www.livestrong.com/article/168904-what-is-the-distance-around-a-running-track-for-each-lane/ below for explanation.

The Distances Around Each Lane
Since the distance around the track in lane one, the inside lane, is 400 meters the distance around the track for the other lanes can be calculated by knowing the lane width and a few other measurements. The formula, L = 2S + 2pi(R + (n-1)w) can be used to calculate the distances around the track for the various lanes. In this formula L equals the lane distance, S equals the length of the straightaway, R is the radius of the turn, n is the lane number and w is the width of the lane.

Since the IAAF has standardized track lane widths at 1.22 meters the above formula calculates the distance around the track in lane 2 as 407.67 meters, lane 3 as 415.33 meters, lane 4 as 423 meters, lane 5 as 430.66 meters, lane 6 as 433.38 meters, lane 7 as 446 meters and lane 8 as 453.66 meters.

Laps in stadiums (on various GPS devices) will always be hit or miss. I would expect a variance of 10-15m per lap as normal.

If you absolutely need to have better tracking of your laps:

Disable auto lap, and mark each lap manually by pressing lap button.

During activity, just run a lane of a known distance and keep your mind only on the timer.

At the end, after the upload, edit the activity to change the total distance.

Use a Stryd for 99.98% accuracy :)