I'd like someone to have a look through these pictures, and see if anything sticks out as being obviously awful.
It is a Arduino board that has onboard SD card, and an onboard RTC.
I used the Arduino schematics, a Adafruit DS3231 schematic, and some forum help from the forum here.
Back copper layer:
That should keep them quiet for a day or so... good job @LarryD
Is there a specific reason for it being 5V logic though ?
Most all stuff you might want to use these days is 3.3V logic, been like that for a good few years too.
Well the AtMega328p-pu runs on 5v at 16mHz. Plus the Uno is 5v, and this is just a modified Uno.
+1
I just had a quick look.
Some of the traces look very close to pads and you don't seem to have used thermal reliefs on pads connected to the ground plane. This could make these difficult to solder. Also, there are lots of unfilled areas which, by adding GND vias, could be filled.
Look again at the charging circuit for the RTC. A lithiuim (non-rechargeable) cell lasts years here so I would not have a charging circuit at all. Don't attempt to charge non-rechargeable cells.
@6v6gt
Thank you for taking the time to look at this! It is much appreciated. Larry's videos are really good too.
I was using a DS3231 circuit that is sold as a module to make this. The area in the black square (u4, D1) is what I would remove to remove the charging circuit, but I tought I'd leave it in to make the board that tiny bit more useful (no battery replacements - seal it up in a project box and never worry about replacing the battery). Is there any reason that it is a bad idea to leave it in?
That would not be a good idea!!
You can read about other peoples experience with the DS3231 and the charging circuit with this Google search: "ds3231 module disable charging circuit"
The rechargeable version of the CR2032 is the LIR2032. It is relatively expensive. That is why the non-rechargeable version is found in some modules with the consequent risk of an explosion.
For some RTCs, I use a super cap (1F to 4F) but also just plain CR2032 (without any charging).
People must be idiotic.
Yeah, I was looking at a $9 one a couple weeks back. 
Note:
I am using a DS3232.
That actually shows me where I went wrong...
The datasheet for the DS3232 says that it is rated for 3.3v, and I had it connected to 5v...
Hi,
Is there any need in your project to use the AT24C32 EEPROM chip?
This chip is present in the DS3231 modules, but is not used by the DS3231.
Your GND plane is all chopped up !
A copper pour on the component side is no longer recommended. <———<<<<
This is all the time I have for this. 
Take a look at how your ground planes are connected together. For instance on the "front copper" the bottom left plane is barely connected to the other planes.
For hobby boards I prefer:
As per the nano schematic, yes.
I downloaded the Eagle files for the Uno, and found that they have a ground pour on both sides.
Again, the nano was not designed with resistors there.
This is not on either the Uno or the Nano schematic.
Again, this isn't in either schematic.
You were offered the suggestions, it’s your project 
.
Nonsense. It's rated at 5.5V max. Oh, you kept saying DS3232, I see now that you are really using a DS3232M.
