I was attempting to create a wizard with a Constitution of 3, and I noticed that the HP was not calculating correctly for both fixed and manual calculations. 

For fixed calculation, whether level 1 or up to level 20, the HP stayed at 2. However, per the basic rules: “Each time you gain a level, you gain 1 additional Hit Die. Roll that Hit Die, add your Constitution modifier to the roll, and add the total (minimum of 1) to your hit point maximum. Alternatively, you can use the fixed value shown in your class entry, which is the average result of the die roll (rounded up).” A minimum of 1 HP should be gained each level. So a level 20 Wizard with 3 Constitution should have 21 HP. 2 HP for level 1 (6 base - 4 for con) and the minimum 1 for each level.
With Manual calculation HP, it got even more weird. If my HP didn’t roll high enough to go beyond the con mod, it could drop to 1 HP. For example 6 hp level 1, then roll a 3 for HP for level 2, I would have 1 HP instead of 3 HP. 

There is no (minimum 1) rule for hit points in dnd unless it is a house rule. Your constitution modifier is -4, and if you are using fixed hit points, the wizard gains 4 hit points + their constitution modifier(-4) which is a total of 0. Therefore, your maximum number of hit points would stay at 2. 

The minimum 1 rule was added to the PHB as errata in October 2020. "Beyond 1st Level (p. 15). In the second sentence of the third paragraph, “add the total” is now “add the total (mini- mum of 1).”" The thing is, there's no 'minimum 1' on the last sentence, regarding using fixed value. The whole point of this errata was to prevent wizards and sorcerers from dying by leveling up, so I'm not sure why the last sentence wasn't changed as well -- possibly they meant it to be implied.

The manual calculation is I guess kind of a follow-on from that -- technically you would have negative HP (following its internal logic) so it's giving you 1 HP to keep you alive.

Strangely, this batch of errata isn't mentioned in this errata thread or this one, though the changes to the text obviously got made. So I'm not sure if the text got changed and no one thought to adjust the builder, or if the hp tracker somehow can't handle this edge case.

I guess for now fudge it with manual rolls of 5?

The problem with the manual rule and the DNDBeyond builder is that it doesn't store your rolled hp per level. It stores it in a pool. So if your rolled HP for a level 3 wizard (before con mod) is 14. It has no idea whether you rolled a 2 and a 6 for level 2 and 3 (which would result in 9 hp with a -2 con modifier) - or if you rolled a 3 and a 5 or two 4's (which would result in 8 hp with a -2 con modifier).

So DNDBeyond keeping the dice in a pool - rather than knowing what each individual roll was - stops them being able to use this errata properly.