Same error here, sometimes I'm stuck on the Mun, sometimes returning from the Mun and splashed down, some times just from orbit. I haven't had a single successful flight (I can't record the progress on my career) since going to 1.12 (five attempts). Here's a log excerpt I think the "collision" lines are interesting. To clarify, this behavior has happened every flight with differing parachute combinations -- I can exit and enter the capsule (I even planted a flag on the Mun once and on another flight I landed and returned to Kerbal splashdown before experiencing the odd behavior). Can't save, can't go to space port, can't go to tracking, can't recover vessel. I end up having to "dump" the game by clicking on another monitor and then closing the window from the task bar.
Captains Log:
[LOG 23:10:37.670] [PartBuoyancy]: Part Z-200 Rechargeable Battery Bank splashed at 9.84397602081299 m/s total, 9.843975 down, effective 9.843975, with tolerance 9.6
[LOG 23:10:37.716] science.module Exploded!! - blast awesomeness: 0.5
[LOG 23:10:37.732] Part HeatShield2 exited collision with COL_Back_Right, but it wasn't in collision count list!
[LOG 23:10:37.732] Part HeatShield2 exited collision with COL_FL_01, but it wasn't in collision count list!
[LOG 23:10:37.732] Part HeatShield2 exited collision with COL_Front, but it wasn't in collision count list!
[LOG 23:10:37.732] Part HeatShield2 exited collision with COL_RR_02, but it wasn't in collision count list!
[LOG 23:10:37.732] Part HeatShield2 exited collision with COL_FL_02, but it wasn't in collision count list!
[LOG 23:10:37.732] Part HeatShield2 exited collision with COL_Front_Left, but it wasn't in collision count list!
[LOG 23:10:37.732] Part HeatShield2 exited collision with COL_FR_01, but it wasn't in collision count list!
[LOG 23:10:37.732] Part HeatShield2 exited collision with COL_RL_01, but it wasn't in collision count list!
[LOG 23:10:37.733] Part HeatShield2 exited collision with COL_Back_Left, but it wasn't in collision count list!
[LOG 23:10:37.733] Part HeatShield2 exited collision with COL_FR_02, but it wasn't in collision count list!
[LOG 23:10:37.733] Part HeatShield2 exited collision with COL_RR_01, but it wasn't in collision count list!
[LOG 23:10:37.733] Part HeatShield2 exited collision with COL_Back, but it wasn't in collision count list!
[LOG 23:10:37.733] Part HeatShield2 exited collision with COL_RL_02, but it wasn't in collision count list!
[LOG 23:10:37.733] Part HeatShield2 exited collision with COL_Front_Right, but it wasn't in collision count list!
[LOG 23:10:37.733] Part HeatShield2 exited collision with Capsule001, but it wasn't in collision count list!
[LOG 23:10:37.763] Part HeatShield2 exited collision with COL_BOT, but it wasn't in collision count list!
[LOG 23:10:38.129] Part HeatShield2 exited collision with Collider, but it wasn't in collision count list!
[LOG 23:10:41.316] [FLIGHT GLOBALS]: Switching To Vessel 2xExploreManned2 ----------------------
[LOG 23:10:41.316] [PlanetariumCamera]: Focus: 2xExploreManned2
[LOG 23:10:41.323] Camera Mode: AUTO
[LOG 23:10:41.356] [FlightGlobals]: ProtoPartSnapShot persistentId changed from 1928990671 to 167246614. Vessel persistentId 0
[LOG 23:10:41.356] [FlightGlobals]: ProtoPartSnapShot persistentId changed from 2524280185 to 814135938. Vessel persistentId 0
[ERR 23:10:43.902] Exception handling event OnVesselRecoveryRequested in class VesselRetrieval:System.ArgumentOutOfRangeException: Index was out of range. Must be non-negative and less than the size of the collection.
Parameter name: index
at System.ThrowHelper.ThrowArgumentOutOfRangeException (System.ExceptionArgument argument, System.ExceptionResource resource) [0x00029] in <9577ac7a62ef43179789031239ba8798>:0
at System.ThrowHelper.ThrowArgumentOutOfRangeException () [0x00000] in <9577ac7a62ef43179789031239ba8798>:0
at Vessel.get_LandedInStockLaunchSite () [0x00086] in <a1ca58b5ca7140639de29a81de5e3f32>:0
at FlightState..ctor () [0x0015b] in <a1ca58b5ca7140639de29a81de5e3f32>:0
at Game.Updated (GameScenes startSceneOverride) [0x0001a] in <a1ca58b5ca7140639de29a81de5e3f32>:0
at GamePersistence.SaveGame (System.String saveFileName, System.String saveFolder, SaveMode saveMode, GameScenes startScene) [0x00045] in <a1ca58b5ca7140639de29a81de5e3f32>:0
at GamePersistence.SaveGame (System.String saveFileName, System.String saveFolder, SaveMode saveMode) [0x00000] in <a1ca58b5ca7140639de29a81de5e3f32>:0
at VesselRetrieval.onVesselRecoveryRequested (Vessel v) [0x0001e] in <a1ca58b5ca7140639de29a81de5e3f32>:0
at EventData`1[T].Fire (T data) [0x000b0] in <a1ca58b5ca7140639de29a81de5e3f32>:0