Violation of PRIMARY KEY constraint 'PK_XY'. Cannot insert duplicate key in object 'dbo.XY'

Using EF Core, I have a Zone that can have multiple Sol (soils), same Sol can be attached to multiple Zone:

public class Sol
{
    // ...  
    public ICollection<Zone> Zones { get; set; } = new List<Zone>();
}

public class Zone
{
    // ...
    public ICollection<Sol> Sols { get; set; } = new List<Sol>();        
}

public override void Configure(EntityTypeBuilder<Zone> builder)
{
    // ...
    builder
        .HasMany(p => p.Sols)
        .WithMany(p => p.Zones);                
}

When adding my Sols to a Zone however I get the following exception:

Microsoft.EntityFrameworkCore.DbUpdateException: An error occurred while updating the entries. See the inner exception for details.

Microsoft.Data.SqlClient.SqlException (0x80131904): Violation of PRIMARY KEY constraint 'PK_SolZone'. Cannot insert duplicate key in object 'dbo.SolZone'. The duplicate key value is (1, 2).

Some details of implementation:

In my controller, when retrieving the object I do

public override async Task<IActionResult> Edit(int id, [FromQuery] bool fullView)
{
    var currentZone = _repository.SingleOrDefault(new GetZoneWithPaysAndSolsSpecification(id));

where

public class GetZoneWithPaysAndSolsSpecification : Specification<Zone>
{
    public GetZoneWithPaysAndSolsSpecification(int zoneId)
    {
        Query.Where(p => p.Id == zoneId);
        Query.Include(p => p.Pays);
        Query.Include(p => p.Sols);
    }
}

before updating the object, I convert my ZoneDTO to Zone and then add it to the database:

protected override void BeforeUpdate(Zone zone, ZoneDTO sourceDto)
{
    zone.Sols.Clear();

    foreach (var solId in sourceDto.SolIds)
    {
        var sol = _repository.GetById<Sol>(solId);
        zone.Sols.Add(sol);
    }

    base.BeforeUpdate(zone, sourceDto);
}

I use the base controller, that uses the BeforeUpdate, like this

[HttpPost]
[ValidateAntiForgeryToken]
public virtual async Task<IActionResult> Edit(TDto dto)
{
    try
    {
        var entity = FromDto(dto);
        BeforeUpdate(entity, dto);
        await _repository.UpdateAsync(entity);
        return RedirectToAction(nameof(Index));
    }
    catch (Exception ex)
    {
        _logger.LogError(ex, "when editing an object after submit");
        return PartialView();
    }
}

The repository code

public Task UpdateAsync<T>(T entity) where T : BaseEntity
{
    _dbContext.Entry(entity).State = EntityState.Modified;
    return _dbContext.SaveChangesAsync();
}

I use AutoMapper

protected TBussinesModel FromDto(TDto dto)
{
    return _mapper.Map<TBussinesModel>(dto);
}

And the mapping is like this

CreateMap<Zone, ZoneDTO>()
    .ForMember(p => p.SolIds, o => o.MapFrom(p => p.Sols.Select(s => s.Id).ToArray()))
    .ForMember(p => p.SolNoms, o => o.MapFrom(p => p.Sols.Select(s => s.Nom).ToArray()))
    .ReverseMap();

When you are mapping from dto to entity, your FromDto method is giving you a Zone entity whose Sols list is not populated with the zone's existing sols. Its an empty list. So, when you are calling -

zone.Sols.Clear();

its doing nothing, and at database level, the zone still holds its sols. Then when you are re-populating the Sols list, you are trying to insert some previously existing Sol to the list.

You have to fetch the existing Zone along with its Sols list from the database, before clearing and repopulating it. How you can do that depends on how your repository is implemented.

On how to update many-to-many entity in EF 5.0, you can check this answer

EDIT :
Try modifying your base controller's Edit method as -

[HttpPost]
[ValidateAntiForgeryToken]
public virtual async Task<IActionResult> Edit(TDto dto)
{
    try
    {
        var zone = _repository.SingleOrDefault(new GetZoneWithPaysAndSolsSpecification(dto.Id));
        
        zone.Sols.Clear();
        
        foreach (var id in dto.SolIds)
        {
            var sol = _repository.GetById<Sol>(solId);
            zone.Sols.Add(sol);
        }

        await _repository.UpdateAsync(zone);
        return RedirectToAction(nameof(Index));
    }
    catch (Exception ex)
    {
        _logger.LogError(ex, "when editing an object after submit");
        return PartialView();
    }
}

Not related to your issue :
You are fetching one Sol a time inside a loop -

foreach (var id in dto.SolIds)
{
    var sol = _repository.GetById<Sol>(solId);
    zone.Sols.Add(sol);
}

which is not efficient at all. Try something like -

var sols = // fetch all the sols from the database
foreach (var id in dto.SolIds)
{
    zone.Sols.Add(sols.FirstOrDefault(p => p.Id == id));
}