The first bug is from a game called "The Shadow" When playing, certain enemies sprites always change between normal and garbled. The garbled sprite is shown below:

I have tested this out on both Snes9x and sneesew and this problem occurs in both of them, it could be a problem with the rom however the checksum does get the all clear from Zsnes. Here is the NSRT info on the rom:
---------------------Internal ROM Info----------------------
File: Shadow, The (U).mgd
Name: THE SHADOW (J) Company: Ocean
Header: None Bank: LoROM
Interleaved: No SRAM: 0 Kb
Type: Normal ROM: 16 Mb
Country: USA Video: NTSC
ROM Speed: 200ns (SlowROM) Version: 1.0
Checksum: Good 0x97E7 CRC32: 36894CC3
--------------------------Database--------------------------
Name: Shadow, The
Country: USA Version: 1.0
Port 1: Gamepad Port 2: Gamepad
The second bug is do with the music in Indiana Jones Greatest Adventures. The problem is that the music just pauses for a split second every now and then for no apparent reason. I played around with the various sound options but none would make any difference. I checked this out in Snes9x and while it does play the music better, it still isn't perfect (some of notes are either 2 short or 2 long). Suprisingly the music worked perfectly in sneesew despite the game having massive graphical problems in that emulator. Here is the NSRT info from the Rom.
---------------------Internal ROM Info----------------------
File: Indiana Jones - Trilogy (E).mgd
Name: INDIANA JONES GREAT Company: JVC
Header: None Bank: LoROM
Interleaved: No SRAM: 0 Kb
Type: Normal ROM: 16 Mb
Country: Euro/Asia/Oceania Video: PAL
ROM Speed: 120ns (FastROM) Version: 1.0
Checksum: Good 0x41CE CRC32: FA4560C3
--------------------------Database--------------------------
Name: Indiana Jones' Greatest Adventures
Country: Europe Version: 1.0
Port 1: Gamepad Port 2: Gamepad
Finally, there is a small graphical glitch in Super Mario Allstars + World. It occurs right at the bottom of the screen (if you take the screenshot from zsnes it doesn't even appear since it is off the actual 'game image'). It is just a single line of a variety of colors as the following screenshot will show you.

Not a major problem obviously but while I was reporting bugs I thought I might as well mention it. This bug does not appear in any other emulator as far as i'm aware and for the record, super mario allstars does not suffer the same problem.
---------------------Internal ROM Info----------------------
File: Super Mario All-Stars & World (E) [!].mgd
Name: MARIO_ALLSTARS+WORLD Company: Nintendo
Header: None Bank: LoROM
Interleaved: No SRAM: 64 Kb
Type: Normal + Batt ROM: 20 Mb
Country: Euro/Asia/Oceania Video: PAL
ROM Speed: 200ns (SlowROM) Version: 1.0
Checksum: Good 0xE9E0 CRC32: 303205D8
--------------------------Database--------------------------
Name: Super Mario All-Stars + Super Mario World
Country: Europe Version: 1.0
Port 1: Gamepad Port 2: Gamepad